PDBx ontology
The PDBx OWL ontology translated from the PDBML schema.
CategoryElement
Abstract class for category elements.
categoryItem
Abstract Datatype property for category items
Abstract property for cross-references.
Abstract property for cross-references between categories.
Abstract property for external links
link to related PDB entry
external link to pubmed
external link to sequence databases
external link to UniProt
external link to GenBank
external link to EMBL
external link to DOI (digital object identifier)
external link to NCBI taxonomy
external link to NCBI taxonomy (source organism)
external link to NCBI taxonomy (host organism)
external link to enzyme code
external link to gene ontology
datablock
DATABLOCK class holds all categories of PDB data.
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Abstract property for xxxCategory.
atom_site
Data items in the ATOM_SITE category record details about
the atom sites in a macromolecular crystal structure, such as
the positional coordinates, atomic displacement parameters,
magnetic moments and directions.
The data items for describing anisotropic atomic
displacement factors are only used if the corresponding items
are not given in the ATOM_SITE_ANISOTROP category.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:atom_siteCategory>
<PDBx:atom_site id="1">
<PDBx:B_iso_or_equiv>17.93</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>25.369</PDBx:Cartn_x>
<PDBx:Cartn_y>30.691</PDBx:Cartn_y>
<PDBx:Cartn_z>11.795</PDBx:Cartn_z>
<PDBx:auth_seq_id>11</PDBx:auth_seq_id>
<PDBx:footnote_id></PDBx:footnote_id>
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id></PDBx:label_alt_id>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>N</PDBx:label_atom_id>
<PDBx:label_comp_id>VAL</PDBx:label_comp_id>
<PDBx:label_seq_id>11</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>N</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="2">
<PDBx:B_iso_or_equiv>17.75</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>25.970</PDBx:Cartn_x>
<PDBx:Cartn_y>31.965</PDBx:Cartn_y>
<PDBx:Cartn_z>12.332</PDBx:Cartn_z>
<PDBx:auth_seq_id>11</PDBx:auth_seq_id>
<PDBx:footnote_id></PDBx:footnote_id>
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id></PDBx:label_alt_id>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>CA</PDBx:label_atom_id>
<PDBx:label_comp_id>VAL</PDBx:label_comp_id>
<PDBx:label_seq_id>11</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="3">
<PDBx:B_iso_or_equiv>17.83</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>25.569</PDBx:Cartn_x>
<PDBx:Cartn_y>32.010</PDBx:Cartn_y>
<PDBx:Cartn_z>13.808</PDBx:Cartn_z>
<PDBx:auth_seq_id>11</PDBx:auth_seq_id>
<PDBx:footnote_id></PDBx:footnote_id>
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id></PDBx:label_alt_id>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>C</PDBx:label_atom_id>
<PDBx:label_comp_id>VAL</PDBx:label_comp_id>
<PDBx:label_seq_id>11</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="4">
<PDBx:B_iso_or_equiv>17.53</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>24.735</PDBx:Cartn_x>
<PDBx:Cartn_y>31.190</PDBx:Cartn_y>
<PDBx:Cartn_z>14.167</PDBx:Cartn_z>
<PDBx:auth_seq_id>11</PDBx:auth_seq_id>
<PDBx:footnote_id></PDBx:footnote_id>
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id></PDBx:label_alt_id>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>O</PDBx:label_atom_id>
<PDBx:label_comp_id>VAL</PDBx:label_comp_id>
<PDBx:label_seq_id>11</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>O</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="5">
<PDBx:B_iso_or_equiv>17.66</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>25.379</PDBx:Cartn_x>
<PDBx:Cartn_y>33.146</PDBx:Cartn_y>
<PDBx:Cartn_z>11.540</PDBx:Cartn_z>
<PDBx:auth_seq_id>11</PDBx:auth_seq_id>
<PDBx:footnote_id></PDBx:footnote_id>
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id></PDBx:label_alt_id>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>CB</PDBx:label_atom_id>
<PDBx:label_comp_id>VAL</PDBx:label_comp_id>
<PDBx:label_seq_id>11</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="6">
<PDBx:B_iso_or_equiv>18.86</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>25.584</PDBx:Cartn_x>
<PDBx:Cartn_y>33.034</PDBx:Cartn_y>
<PDBx:Cartn_z>10.030</PDBx:Cartn_z>
<PDBx:auth_seq_id>11</PDBx:auth_seq_id>
<PDBx:footnote_id></PDBx:footnote_id>
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id></PDBx:label_alt_id>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>CG1</PDBx:label_atom_id>
<PDBx:label_comp_id>VAL</PDBx:label_comp_id>
<PDBx:label_seq_id>11</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="7">
<PDBx:B_iso_or_equiv>17.12</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>23.933</PDBx:Cartn_x>
<PDBx:Cartn_y>33.309</PDBx:Cartn_y>
<PDBx:Cartn_z>11.872</PDBx:Cartn_z>
<PDBx:auth_seq_id>11</PDBx:auth_seq_id>
<PDBx:footnote_id></PDBx:footnote_id>
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id></PDBx:label_alt_id>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>CG2</PDBx:label_atom_id>
<PDBx:label_comp_id>VAL</PDBx:label_comp_id>
<PDBx:label_seq_id>11</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="8">
<PDBx:B_iso_or_equiv>18.97</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>26.095</PDBx:Cartn_x>
<PDBx:Cartn_y>32.930</PDBx:Cartn_y>
<PDBx:Cartn_z>14.590</PDBx:Cartn_z>
<PDBx:auth_seq_id>12</PDBx:auth_seq_id>
<PDBx:footnote_id>4</PDBx:footnote_id>
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id></PDBx:label_alt_id>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>N</PDBx:label_atom_id>
<PDBx:label_comp_id>THR</PDBx:label_comp_id>
<PDBx:label_seq_id>12</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>N</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="9">
<PDBx:B_iso_or_equiv>19.80</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>25.734</PDBx:Cartn_x>
<PDBx:Cartn_y>32.995</PDBx:Cartn_y>
<PDBx:Cartn_z>16.032</PDBx:Cartn_z>
<PDBx:auth_seq_id>12</PDBx:auth_seq_id>
<PDBx:footnote_id>4</PDBx:footnote_id>
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id></PDBx:label_alt_id>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>CA</PDBx:label_atom_id>
<PDBx:label_comp_id>THR</PDBx:label_comp_id>
<PDBx:label_seq_id>12</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="10">
<PDBx:B_iso_or_equiv>20.92</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>24.695</PDBx:Cartn_x>
<PDBx:Cartn_y>34.106</PDBx:Cartn_y>
<PDBx:Cartn_z>16.113</PDBx:Cartn_z>
<PDBx:auth_seq_id>12</PDBx:auth_seq_id>
<PDBx:footnote_id>4</PDBx:footnote_id>
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id></PDBx:label_alt_id>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>C</PDBx:label_atom_id>
<PDBx:label_comp_id>THR</PDBx:label_comp_id>
<PDBx:label_seq_id>12</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="11">
<PDBx:B_iso_or_equiv>21.84</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>24.869</PDBx:Cartn_x>
<PDBx:Cartn_y>35.118</PDBx:Cartn_y>
<PDBx:Cartn_z>15.421</PDBx:Cartn_z>
<PDBx:auth_seq_id>12</PDBx:auth_seq_id>
<PDBx:footnote_id>4</PDBx:footnote_id>
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id></PDBx:label_alt_id>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>O</PDBx:label_atom_id>
<PDBx:label_comp_id>THR</PDBx:label_comp_id>
<PDBx:label_seq_id>12</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>O</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="12">
<PDBx:B_iso_or_equiv>20.51</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>26.911</PDBx:Cartn_x>
<PDBx:Cartn_y>33.346</PDBx:Cartn_y>
<PDBx:Cartn_z>17.018</PDBx:Cartn_z>
<PDBx:auth_seq_id>12</PDBx:auth_seq_id>
<PDBx:footnote_id>4</PDBx:footnote_id>
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id></PDBx:label_alt_id>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>CB</PDBx:label_atom_id>
<PDBx:label_comp_id>THR</PDBx:label_comp_id>
<PDBx:label_seq_id>12</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="13">
<PDBx:B_iso_or_equiv>20.29</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>27.946</PDBx:Cartn_x>
<PDBx:Cartn_y>33.921</PDBx:Cartn_y>
<PDBx:Cartn_z>16.183</PDBx:Cartn_z>
<PDBx:auth_seq_id>12</PDBx:auth_seq_id>
<PDBx:footnote_id>4</PDBx:footnote_id>
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id>3</PDBx:label_alt_id>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>OG1</PDBx:label_atom_id>
<PDBx:label_comp_id>THR</PDBx:label_comp_id>
<PDBx:label_seq_id>12</PDBx:label_seq_id>
<PDBx:occupancy>0.50</PDBx:occupancy>
<PDBx:type_symbol>O</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="14">
<PDBx:B_iso_or_equiv>20.59</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>27.769</PDBx:Cartn_x>
<PDBx:Cartn_y>32.142</PDBx:Cartn_y>
<PDBx:Cartn_z>17.103</PDBx:Cartn_z>
<PDBx:auth_seq_id>12</PDBx:auth_seq_id>
<PDBx:footnote_id>4</PDBx:footnote_id>
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id>4</PDBx:label_alt_id>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>OG1</PDBx:label_atom_id>
<PDBx:label_comp_id>THR</PDBx:label_comp_id>
<PDBx:label_seq_id>12</PDBx:label_seq_id>
<PDBx:occupancy>0.50</PDBx:occupancy>
<PDBx:type_symbol>O</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="15">
<PDBx:B_iso_or_equiv>20.47</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>27.418</PDBx:Cartn_x>
<PDBx:Cartn_y>32.181</PDBx:Cartn_y>
<PDBx:Cartn_z>17.878</PDBx:Cartn_z>
<PDBx:auth_seq_id>12</PDBx:auth_seq_id>
<PDBx:footnote_id>4</PDBx:footnote_id>
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id>3</PDBx:label_alt_id>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>CG2</PDBx:label_atom_id>
<PDBx:label_comp_id>THR</PDBx:label_comp_id>
<PDBx:label_seq_id>12</PDBx:label_seq_id>
<PDBx:occupancy>0.50</PDBx:occupancy>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="16">
<PDBx:B_iso_or_equiv>20.00</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>26.489</PDBx:Cartn_x>
<PDBx:Cartn_y>33.778</PDBx:Cartn_y>
<PDBx:Cartn_z>18.426</PDBx:Cartn_z>
<PDBx:auth_seq_id>12</PDBx:auth_seq_id>
<PDBx:footnote_id>4</PDBx:footnote_id>
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id>4</PDBx:label_alt_id>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>CG2</PDBx:label_atom_id>
<PDBx:label_comp_id>THR</PDBx:label_comp_id>
<PDBx:label_seq_id>12</PDBx:label_seq_id>
<PDBx:occupancy>0.50</PDBx:occupancy>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="17">
<PDBx:B_iso_or_equiv>22.08</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>23.664</PDBx:Cartn_x>
<PDBx:Cartn_y>33.855</PDBx:Cartn_y>
<PDBx:Cartn_z>16.884</PDBx:Cartn_z>
<PDBx:auth_seq_id>13</PDBx:auth_seq_id>
<PDBx:footnote_id></PDBx:footnote_id>
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id></PDBx:label_alt_id>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>N</PDBx:label_atom_id>
<PDBx:label_comp_id>ILE</PDBx:label_comp_id>
<PDBx:label_seq_id>13</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>N</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="18">
<PDBx:B_iso_or_equiv>23.44</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>22.623</PDBx:Cartn_x>
<PDBx:Cartn_y>34.850</PDBx:Cartn_y>
<PDBx:Cartn_z>17.093</PDBx:Cartn_z>
<PDBx:auth_seq_id>13</PDBx:auth_seq_id>
<PDBx:footnote_id></PDBx:footnote_id>
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id></PDBx:label_alt_id>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>CA</PDBx:label_atom_id>
<PDBx:label_comp_id>ILE</PDBx:label_comp_id>
<PDBx:label_seq_id>13</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="19">
<PDBx:B_iso_or_equiv>25.77</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>22.657</PDBx:Cartn_x>
<PDBx:Cartn_y>35.113</PDBx:Cartn_y>
<PDBx:Cartn_z>18.610</PDBx:Cartn_z>
<PDBx:auth_seq_id>13</PDBx:auth_seq_id>
<PDBx:footnote_id></PDBx:footnote_id>
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id></PDBx:label_alt_id>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>C</PDBx:label_atom_id>
<PDBx:label_comp_id>ILE</PDBx:label_comp_id>
<PDBx:label_seq_id>13</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="20">
<PDBx:B_iso_or_equiv>26.28</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>23.123</PDBx:Cartn_x>
<PDBx:Cartn_y>34.250</PDBx:Cartn_y>
<PDBx:Cartn_z>19.406</PDBx:Cartn_z>
<PDBx:auth_seq_id>13</PDBx:auth_seq_id>
<PDBx:footnote_id></PDBx:footnote_id>
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id></PDBx:label_alt_id>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>O</PDBx:label_atom_id>
<PDBx:label_comp_id>ILE</PDBx:label_comp_id>
<PDBx:label_seq_id>13</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>O</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="21">
<PDBx:B_iso_or_equiv>22.67</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>21.236</PDBx:Cartn_x>
<PDBx:Cartn_y>34.463</PDBx:Cartn_y>
<PDBx:Cartn_z>16.492</PDBx:Cartn_z>
<PDBx:auth_seq_id>13</PDBx:auth_seq_id>
<PDBx:footnote_id></PDBx:footnote_id>
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id></PDBx:label_alt_id>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>CB</PDBx:label_atom_id>
<PDBx:label_comp_id>ILE</PDBx:label_comp_id>
<PDBx:label_seq_id>13</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="22">
<PDBx:B_iso_or_equiv>22.14</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>20.478</PDBx:Cartn_x>
<PDBx:Cartn_y>33.469</PDBx:Cartn_y>
<PDBx:Cartn_z>17.371</PDBx:Cartn_z>
<PDBx:auth_seq_id>13</PDBx:auth_seq_id>
<PDBx:footnote_id></PDBx:footnote_id>
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id></PDBx:label_alt_id>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>CG1</PDBx:label_atom_id>
<PDBx:label_comp_id>ILE</PDBx:label_comp_id>
<PDBx:label_seq_id>13</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="23">
<PDBx:B_iso_or_equiv>21.75</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>21.357</PDBx:Cartn_x>
<PDBx:Cartn_y>33.986</PDBx:Cartn_y>
<PDBx:Cartn_z>15.016</PDBx:Cartn_z>
<PDBx:auth_seq_id>13</PDBx:auth_seq_id>
<PDBx:footnote_id></PDBx:footnote_id>
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:label_alt_id></PDBx:label_alt_id>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_atom_id>CG2</PDBx:label_atom_id>
<PDBx:label_comp_id>ILE</PDBx:label_comp_id>
<PDBx:label_seq_id>13</PDBx:label_seq_id>
<PDBx:occupancy>1.00</PDBx:occupancy>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="101">
<PDBx:B_iso_or_equiv>17.27</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>4.171</PDBx:Cartn_x>
<PDBx:Cartn_y>29.012</PDBx:Cartn_y>
<PDBx:Cartn_z>7.116</PDBx:Cartn_z>
<PDBx:auth_seq_id>300</PDBx:auth_seq_id>
<PDBx:footnote_id>1</PDBx:footnote_id>
<PDBx:group_PDB>HETATM</PDBx:group_PDB>
<PDBx:label_alt_id>1</PDBx:label_alt_id>
<PDBx:label_asym_id>C</PDBx:label_asym_id>
<PDBx:label_atom_id>C1</PDBx:label_atom_id>
<PDBx:label_comp_id>APS</PDBx:label_comp_id>
<PDBx:label_seq_id></PDBx:label_seq_id>
<PDBx:occupancy>0.58</PDBx:occupancy>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="102">
<PDBx:B_iso_or_equiv>16.95</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>4.949</PDBx:Cartn_x>
<PDBx:Cartn_y>27.758</PDBx:Cartn_y>
<PDBx:Cartn_z>6.793</PDBx:Cartn_z>
<PDBx:auth_seq_id>300</PDBx:auth_seq_id>
<PDBx:footnote_id>1</PDBx:footnote_id>
<PDBx:group_PDB>HETATM</PDBx:group_PDB>
<PDBx:label_alt_id>1</PDBx:label_alt_id>
<PDBx:label_asym_id>C</PDBx:label_asym_id>
<PDBx:label_atom_id>C2</PDBx:label_atom_id>
<PDBx:label_comp_id>APS</PDBx:label_comp_id>
<PDBx:label_seq_id></PDBx:label_seq_id>
<PDBx:occupancy>0.58</PDBx:occupancy>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="103">
<PDBx:B_iso_or_equiv>16.85</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>4.800</PDBx:Cartn_x>
<PDBx:Cartn_y>26.678</PDBx:Cartn_y>
<PDBx:Cartn_z>7.393</PDBx:Cartn_z>
<PDBx:auth_seq_id>300</PDBx:auth_seq_id>
<PDBx:footnote_id>1</PDBx:footnote_id>
<PDBx:group_PDB>HETATM</PDBx:group_PDB>
<PDBx:label_alt_id>1</PDBx:label_alt_id>
<PDBx:label_asym_id>C</PDBx:label_asym_id>
<PDBx:label_atom_id>O3</PDBx:label_atom_id>
<PDBx:label_comp_id>APS</PDBx:label_comp_id>
<PDBx:label_seq_id></PDBx:label_seq_id>
<PDBx:occupancy>0.58</PDBx:occupancy>
<PDBx:type_symbol>O</PDBx:type_symbol>
</PDBx:atom_site>
<PDBx:atom_site id="104">
<PDBx:B_iso_or_equiv>16.43</PDBx:B_iso_or_equiv>
<PDBx:Cartn_x>5.930</PDBx:Cartn_x>
<PDBx:Cartn_y>27.841</PDBx:Cartn_y>
<PDBx:Cartn_z>5.869</PDBx:Cartn_z>
<PDBx:auth_seq_id>300</PDBx:auth_seq_id>
<PDBx:footnote_id>1</PDBx:footnote_id>
<PDBx:group_PDB>HETATM</PDBx:group_PDB>
<PDBx:label_alt_id>1</PDBx:label_alt_id>
<PDBx:label_asym_id>C</PDBx:label_asym_id>
<PDBx:label_atom_id>N4</PDBx:label_atom_id>
<PDBx:label_comp_id>APS</PDBx:label_comp_id>
<PDBx:label_seq_id></PDBx:label_seq_id>
<PDBx:occupancy>0.58</PDBx:occupancy>
<PDBx:type_symbol>N</PDBx:type_symbol>
</PDBx:atom_site>
</PDBx:atom_siteCategory>
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atom_siteCategory
This property indicates that datablock
has a category element atom_site.
atom_siteItem
Abstract Datatype property for atom_site items.
reference_to_atom_site
cross-reference to atom_site
atom_site.B_equiv_geom_mean
Equivalent isotropic atomic displacement parameter, B~eq~,
in angstroms squared, calculated as the geometric mean of
the anisotropic atomic displacement parameters.
B~eq~ = (B~i~ B~j~ B~k~)^1/3^
B~n~ = the principal components of the orthogonalized B^ij^
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
atom_site.B_equiv_geom_mean_esd
The standard uncertainty (estimated standard deviation)
of attribute B_equiv_geom_mean in category atom_site.
atom_site.B_iso_or_equiv
Isotropic atomic displacement parameter, or equivalent isotropic
atomic displacement parameter, B~eq~, calculated from the
anisotropic displacement parameters.
B~eq~ = (1/3) sum~i~[sum~j~(B^ij^ A~i~ A~j~ a*~i~ a*~j~)]
A = the real space cell lengths
a* = the reciprocal space cell lengths
B^ij^ = 8 pi^2^ U^ij^
Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44,
775-776.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
atom_site.B_iso_or_equiv_esd
The standard uncertainty (estimated standard deviation)
of attribute B_iso_or_equiv in category atom_site.
atom_site.Cartn_x
The x atom-site coordinate in angstroms specified according to
a set of orthogonal Cartesian axes related to the cell axes as
specified by the description given in
attribute Cartn_transform_axes in category atom_sites.
atom_site.Cartn_x_esd
The standard uncertainty (estimated standard deviation)
of attribute Cartn_x in category atom_site.
atom_site.Cartn_y
The y atom-site coordinate in angstroms specified according to
a set of orthogonal Cartesian axes related to the cell axes as
specified by the description given in
attribute Cartn_transform_axes in category atom_sites.
atom_site.Cartn_y_esd
The standard uncertainty (estimated standard deviation)
of attribute Cartn_y in category atom_site.
atom_site.Cartn_z
The z atom-site coordinate in angstroms specified according to
a set of orthogonal Cartesian axes related to the cell axes as
specified by the description given in
attribute Cartn_transform_axes in category atom_sites.
atom_site.Cartn_z_esd
The standard uncertainty (estimated standard deviation)
of attribute Cartn_z in category atom_site.
atom_site.U_equiv_geom_mean
Equivalent isotropic atomic displacement parameter, U~eq~,
in angstroms squared, calculated as the geometric mean of
the anisotropic atomic displacement parameters.
U~eq~ = (U~i~ U~j~ U~k~)^1/3^
U~n~ = the principal components of the orthogonalized U^ij^
atom_site.U_equiv_geom_mean_esd
The standard uncertainty (estimated standard deviation)
of attribute U_equiv_geom_mean in category atom_site.
atom_site.U_iso_or_equiv
Isotropic atomic displacement parameter, or equivalent isotropic
atomic displacement parameter, U~eq~, calculated from
anisotropic atomic displacement parameters.
U~eq~ = (1/3) sum~i~[sum~j~(U^ij^ A~i~ A~j~ a*~i~ a*~j~)]
A = the real space cell lengths
a* = the reciprocal space cell lengths
Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44,
775-776.
atom_site.U_iso_or_equiv_esd
The standard uncertainty (estimated standard deviation)
of attribute U_iso_or_equiv in category atom_site.
atom_site.Wyckoff_symbol
The Wyckoff symbol (letter) as listed in the space-group tables
of International Tables for Crystallography, Vol. A (2002).
Uani
Uiso
Uovl
Umpe
Bani
Biso
Bovl
A standard code used to describe the type of atomic displacement
parameters used for the site.
atom_site.aniso_B11
The [1][1] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
atom_site.aniso_B11_esd
The standard uncertainty (estimated standard deviation)
of attribute aniso_B[1][1] in category atom_site.
atom_site.aniso_B12
The [1][2] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
atom_site.aniso_B12_esd
The standard uncertainty (estimated standard deviation)
of attribute aniso_B[1][2] in category atom_site.
atom_site.aniso_B13
The [1][3] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
atom_site.aniso_B13_esd
The standard uncertainty (estimated standard deviation)
of attribute aniso_B[1][3] in category atom_site.
atom_site.aniso_B22
The [2][2] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
atom_site.aniso_B22_esd
The standard uncertainty (estimated standard deviation)
of attribute aniso_B[2][2] in category atom_site.
atom_site.aniso_B23
The [2][3] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
atom_site.aniso_B23_esd
The standard uncertainty (estimated standard deviation)
of attribute aniso_B[2][3] in category atom_site.
atom_site.aniso_B33
The [3][3] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
atom_site.aniso_B33_esd
The standard uncertainty (estimated standard deviation)
of attribute aniso_B[3][3] in category atom_site.
atom_site.aniso_U11
The [1][1] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
atom_site.aniso_U11_esd
The standard uncertainty (estimated standard deviation)
of attribute aniso_U[1][1] in category atom_site.
atom_site.aniso_U12
The [1][2] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
atom_site.aniso_U12_esd
The standard uncertainty (estimated standard deviation)
of attribute aniso_U[1][2] in category atom_site.
atom_site.aniso_U13
The [1][3] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
atom_site.aniso_U13_esd
The standard uncertainty (estimated standard deviation)
of attribute aniso_U[1][3] in category atom_site.
atom_site.aniso_U22
The [2][2] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
atom_site.aniso_U22_esd
The standard uncertainty (estimated standard deviation)
of attribute aniso_U[2][2] in category atom_site.
atom_site.aniso_U23
The [2][3] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
atom_site.aniso_U23_esd
The standard uncertainty (estimated standard deviation)
of attribute aniso_U[2][3] in category atom_site.
atom_site.aniso_U33
The [3][3] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
atom_site.aniso_U33_esd
The standard uncertainty (estimated standard deviation)
of attribute aniso_U[3][3] in category atom_site.
atom_site.aniso_ratio
Ratio of the maximum to minimum principal axes of
displacement (thermal) ellipsoids.
atom_site.attached_hydrogens
The number of hydrogen atoms attached to the atom at this site
excluding any hydrogen atoms for which coordinates (measured or
calculated) are given.
water oxygen
2
hydroxyl oxygen
1
ammonium nitrogen
4
atom_site.auth_asym_id
An alternative identifier for attribute label_asym_id in category atom_site that
may be provided by an author in order to match the identification
used in the publication that describes the structure.
atom_site.auth_atom_id
An alternative identifier for attribute label_atom_id in category atom_site that
may be provided by an author in order to match the identification
used in the publication that describes the structure.
atom_site.auth_comp_id
An alternative identifier for attribute label_comp_id in category atom_site that
may be provided by an author in order to match the identification
used in the publication that describes the structure.
atom_site.auth_seq_id
An alternative identifier for attribute label_seq_id in category atom_site that
may be provided by an author in order to match the identification
used in the publication that describes the structure.
Note that this is not necessarily a number, that the values do
not have to be positive, and that the value does not have to
correspond to the value of attribute label_seq_id in category atom_site. The value
of attribute label_seq_id in category atom_site is required to be a sequential list
of positive integers.
The author may assign values to attribute auth_seq_id in category atom_site in any
desired way. For instance, the values may be used to relate
this structure to a numbering scheme in a homologous structure,
including sequence gaps or insertion codes. Alternatively, a
scheme may be used for a truncated polymer that maintains the
numbering scheme of the full length polymer. In all cases, the
scheme used here must match the scheme used in the publication
that describes the structure.
atom_site.calc_attached_atom
The attribute id in category atom_site of the atom site to which the
'geometry-calculated' atom site is attached.
d
calc
c
dum
A standard code to signal whether the site coordinates have been
determined from the intensities or calculated from the geometry
of surrounding sites, or have been assigned dummy values. The
abbreviation 'c' may be used in place of 'calc'.
atom_site.chemical_conn_number
This data item is a pointer to attribute number in category chemical_conn_atom in the
CHEMICAL_CONN_ATOM category.
atom_site.constraints
A description of the constraints applied to parameters at this
site during refinement. See also attribute refinement_flags
in category atom_site and attribute ls_number_constraints in category refine.
pop=1.0-pop(Zn3)
atom_site.details
A description of special aspects of this site. See also
attribute refinement_flags in category atom_site.
Ag/Si disordered
atom_site.disorder_assembly
A code which identifies a cluster of atoms that show long-range
positional disorder but are locally ordered. Within each such
cluster of atoms, attribute disorder_group in category atom_site is used to identify
the sites that are simultaneously occupied. This field is only
needed if there is more than one cluster of disordered atoms
showing independent local order.
*** This data item would not in general be used in a
macromolecular data block. ***
atom_site.disorder_group
A code which identifies a group of positionally disordered atom
sites that are locally simultaneously occupied. Atoms that are
positionally disordered over two or more sites (e.g. the hydrogen
atoms of a methyl group that exists in two orientations) can
be assigned to two or more groups. Sites belonging to the same
group are simultaneously occupied, but those belonging to
different groups are not. A minus prefix (e.g. '-1') is used to
indicate sites disordered about a special position.
*** This data item would not in general be used in a
macromolecular data block. ***
atom_site.footnote_id
The value of attribute footnote_id in category atom_site must match an ID
specified by attribute id in category atom_sites_footnote in the
ATOM_SITES_FOOTNOTE list.
atom_site.fract_x
The x coordinate of the atom-site position specified as a
fraction of attribute length_a in category cell.
atom_site.fract_x_esd
The standard uncertainty (estimated standard deviation)
of attribute fract_x in category atom_site.
atom_site.fract_y
The y coordinate of the atom-site position specified as a
fraction of attribute length_b in category cell.
atom_site.fract_y_esd
The standard uncertainty (estimated standard deviation)
of attribute fract_y in category atom_site.
atom_site.fract_z
The z coordinate of the atom-site position specified as a
fraction of attribute length_c in category cell.
atom_site.fract_z_esd
The standard uncertainty (estimated standard deviation)
of attribute fract_z in category atom_site.
ATOM
HETATM
The group of atoms to which the atom site belongs. This data
item is provided for compatibility with the original Protein
Data Bank format, and only for that purpose.
atom_site.label_alt_id
A component of the identifier for this atom site.
For further details, see the definition of the ATOM_SITE_ALT
category.
This data item is a pointer to attribute id in category atom_sites_alt in the
ATOM_SITES_ALT category.
atom_site.label_asym_id
A component of the identifier for this atom site.
For further details, see the definition of the STRUCT_ASYM
category.
This data item is a pointer to attribute id in category struct_asym in the
STRUCT_ASYM category.
atom_site.label_atom_id
A component of the identifier for this atom site.
This data item is a pointer to attribute atom_id in category chem_comp_atom in the
CHEM_COMP_ATOM category.
atom_site.label_comp_id
A component of the identifier for this atom site.
This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP
category.
atom_site.label_entity_id
This data item is a pointer to attribute id in category entity in the ENTITY category.
atom_site.label_seq_id
This data item is a pointer to attribute num in category entity_poly_seq in the
ENTITY_POLY_SEQ category.
atom_site.occupancy
The fraction of the atom type present at this site.
The sum of the occupancies of all the atom types at this site
may not significantly exceed 1.0 unless it is a dummy site.
atom_site.occupancy_esd
The standard uncertainty (estimated standard deviation)
of attribute occupancy in category atom_site.
atom_site.pdbx_PDB_atom_name
PDB atom name.
atom_site.pdbx_PDB_ins_code
PDB insertion code.
atom_site.pdbx_PDB_model_num
PDB model number.
atom_site.pdbx_PDB_residue_name
PDB residue name.
atom_site.pdbx_PDB_residue_no
PDB residue number.
atom_site.pdbx_PDB_strand_id
PDB strand id.
atom_site.pdbx_auth_alt_id
Author's alternate location identifier.
atom_site.pdbx_auth_atom_name
Author's atom name.
atom_site.pdbx_formal_charge
The net integer charge assigned to this atom. This is the
formal charge assignment normally found in chemical diagrams.
for an ammonium nitrogen
1
for a chloride ion
-1
atom_site.pdbx_ncs_dom_id
The NCS domain to which the atom position is assigned.
The NCS group is defined in category struct_ncs_dom.
This item is a reference to attribute id in category struct_ncs_dom.
atom_site.pdbx_tls_group_id
The TLS group to which the atom position is assigned.
The TLS group is defined in category pdbx_refine_tls.
This item is a reference to attribute id in category pdbx_refine_tls.
S
G
R
D
T
U
P
A concatenated series of single-letter codes which indicate the
refinement restraints or constraints applied to this site. This
item should not be used. It has been replaced by
attribute refinement_flags_posn in category atom_site, *_adp and *_occupancy. It is
retained in this dictionary only to provide compatibility with
old CIFs.
T
U
TU
A code which indicates the refinement restraints or constraints
applied to the atomic displacement parameters of this site.
P
A code which indicates that refinement restraints or
constraints were applied to the occupancy of this site.
D
G
R
S
DG
DR
DS
GR
GS
RS
DGR
DGS
DRS
GRS
DGRS
A code which indicates the refinement restraints or constraints
applied to the positional coordinates of this site.
atom_site.restraints
A description of restraints applied to specific parameters at
this site during refinement. See also attribute refinement_flags
in category atom_site and attribute ls_number_restraints in category refine.
restrained to planar ring
atom_site.symmetry_multiplicity
The multiplicity of a site due to the space-group symmetry as is
given in International Tables for Crystallography Vol. A (2002).
Uani
Uiso
Uovl
Umpe
Bani
Biso
Bovl
A standard code used to describe the type of atomic displacement
parameters used for the site.
atom_site.type_symbol
This data item is a pointer to attribute symbol in category atom_type in the
ATOM_TYPE category.
atom_site.id
The value of attribute id in category atom_site must uniquely identify a record in the
ATOM_SITE list.
Note that this item need not be a number; it can be any unique
identifier.
This data item was introduced to provide compatibility between
small-molecule and macromolecular CIFs. In a small-molecule
CIF, _atom_site_label is the identifier for the atom. In a
macromolecular CIF, the atom identifier is the aggregate of
_atom_site.label_alt_id, _atom_site.label_asym_id,
_atom_site.label_atom_id, _atom_site.label_comp_id and
attribute label_seq_id in category atom_site. For the two types of files to be
compatible, a formal identifier for the category had to be
introduced that was independent of the different modes of
identifying the atoms. For compatibility with older CIFs,
_atom_site_label is aliased to attribute id in category atom_site.
5
C12
Ca3g28
Fe3+17
H*251
boron2a
C_a_phe_83_a_0
Zn_Zn_301_A_0
atom_site_anisotrop
Data items in the ATOM_SITE_ANISOTROP category record details
about anisotropic displacement parameters.
If the ATOM_SITE_ANISOTROP category is used for storing these
data, the corresponding ATOM_SITE data items are not used.
Example 1 - based on NDB structure BDL005 of Holbrook, Dickerson &
Kim [Acta Cryst. (1985), B41, 255-262].
<PDBx:atom_site_anisotropCategory>
<PDBx:atom_site_anisotrop id="1">
<PDBx:U11>8642</PDBx:U11>
<PDBx:U12>4866</PDBx:U12>
<PDBx:U13>7299</PDBx:U13>
<PDBx:U22>-342</PDBx:U22>
<PDBx:U23>-258</PDBx:U23>
<PDBx:U33>-1427</PDBx:U33>
<PDBx:type_symbol>O</PDBx:type_symbol>
</PDBx:atom_site_anisotrop>
<PDBx:atom_site_anisotrop id="2">
<PDBx:U11>5174</PDBx:U11>
<PDBx:U12>4871</PDBx:U12>
<PDBx:U13>6243</PDBx:U13>
<PDBx:U22>-1885</PDBx:U22>
<PDBx:U23>-2051</PDBx:U23>
<PDBx:U33>-1377</PDBx:U33>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site_anisotrop>
<PDBx:atom_site_anisotrop id="3">
<PDBx:U11>6202</PDBx:U11>
<PDBx:U12>5020</PDBx:U12>
<PDBx:U13>4395</PDBx:U13>
<PDBx:U22>-1130</PDBx:U22>
<PDBx:U23>-556</PDBx:U23>
<PDBx:U33>-632</PDBx:U33>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site_anisotrop>
<PDBx:atom_site_anisotrop id="4">
<PDBx:U11>4224</PDBx:U11>
<PDBx:U12>4700</PDBx:U12>
<PDBx:U13>5046</PDBx:U13>
<PDBx:U22>1105</PDBx:U22>
<PDBx:U23>-161</PDBx:U23>
<PDBx:U33>345</PDBx:U33>
<PDBx:type_symbol>O</PDBx:type_symbol>
</PDBx:atom_site_anisotrop>
<PDBx:atom_site_anisotrop id="5">
<PDBx:U11>8684</PDBx:U11>
<PDBx:U12>4688</PDBx:U12>
<PDBx:U13>4171</PDBx:U13>
<PDBx:U22>-1850</PDBx:U22>
<PDBx:U23>-433</PDBx:U23>
<PDBx:U33>-292</PDBx:U33>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site_anisotrop>
<PDBx:atom_site_anisotrop id="6">
<PDBx:U11>11226</PDBx:U11>
<PDBx:U12>5255</PDBx:U12>
<PDBx:U13>3532</PDBx:U13>
<PDBx:U22>-341</PDBx:U22>
<PDBx:U23>2685</PDBx:U23>
<PDBx:U33>1328</PDBx:U33>
<PDBx:type_symbol>O</PDBx:type_symbol>
</PDBx:atom_site_anisotrop>
<PDBx:atom_site_anisotrop id="7">
<PDBx:U11>10214</PDBx:U11>
<PDBx:U12>2428</PDBx:U12>
<PDBx:U13>5614</PDBx:U13>
<PDBx:U22>-2610</PDBx:U22>
<PDBx:U23>-1940</PDBx:U23>
<PDBx:U33>902</PDBx:U33>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site_anisotrop>
<PDBx:atom_site_anisotrop id="8">
<PDBx:U11>4590</PDBx:U11>
<PDBx:U12>3488</PDBx:U12>
<PDBx:U13>5827</PDBx:U13>
<PDBx:U22>751</PDBx:U22>
<PDBx:U23>-770</PDBx:U23>
<PDBx:U33>986</PDBx:U33>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:atom_site_anisotrop>
<PDBx:atom_site_anisotrop id="9">
<PDBx:U11>5014</PDBx:U11>
<PDBx:U12>4434</PDBx:U12>
<PDBx:U13>3447</PDBx:U13>
<PDBx:U22>-17</PDBx:U22>
<PDBx:U23>-1593</PDBx:U23>
<PDBx:U33>539</PDBx:U33>
<PDBx:type_symbol>N</PDBx:type_symbol>
</PDBx:atom_site_anisotrop>
</PDBx:atom_site_anisotropCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
atom_site_anisotropCategory
This property indicates that datablock
has a category element atom_site_anisotrop.
atom_site_anisotropItem
Abstract Datatype property for atom_site_anisotrop items.
reference_to_atom_site_anisotrop
cross-reference to atom_site_anisotrop
atom_site_anisotrop.B11
The [1][1] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
atom_site_anisotrop.B11_esd
The standard uncertainty (estimated standard deviation)
of attribute B[1][1] in category atom_site_anisotrop.
atom_site_anisotrop.B12
The [1][2] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
atom_site_anisotrop.B12_esd
The standard uncertainty (estimated standard deviation)
of attribute B[1][2] in category atom_site_anisotrop.
atom_site_anisotrop.B13
The [1][3] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
atom_site_anisotrop.B13_esd
The standard uncertainty (estimated standard deviation)
of attribute B[1][3] in category atom_site_anisotrop.
atom_site_anisotrop.B22
The [2][2] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
atom_site_anisotrop.B22_esd
The standard uncertainty (estimated standard deviation)
of attribute B[2][2] in category atom_site_anisotrop.
atom_site_anisotrop.B23
The [2][3] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
atom_site_anisotrop.B23_esd
The standard uncertainty (estimated standard deviation)
of attribute B[2][3] in category atom_site_anisotrop.
atom_site_anisotrop.B33
The [3][3] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
atom_site_anisotrop.B33_esd
The standard uncertainty (estimated standard deviation)
of attribute B[3][3] in category atom_site_anisotrop.
atom_site_anisotrop.U11
The [1][1] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
atom_site_anisotrop.U11_esd
The standard uncertainty (estimated standard deviation)
of attribute U[1][1] in category atom_site_anisotrop.
atom_site_anisotrop.U12
The [1][2] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
atom_site_anisotrop.U12_esd
The standard uncertainty (estimated standard deviation)
of attribute U[1][2] in category atom_site_anisotrop.
atom_site_anisotrop.U13
The [1][3] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
atom_site_anisotrop.U13_esd
The standard uncertainty (estimated standard deviation)
of attribute U[1][3] in category atom_site_anisotrop.
atom_site_anisotrop.U22
The [2][2] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
atom_site_anisotrop.U22_esd
The standard uncertainty (estimated standard deviation)
of attribute U[2][2] in category atom_site_anisotrop.
atom_site_anisotrop.U23
The [2][3] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
atom_site_anisotrop.U23_esd
The standard uncertainty (estimated standard deviation)
of attribute U[2][3] in category atom_site_anisotrop.
atom_site_anisotrop.U33
The [3][3] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
atom_site_anisotrop.U33_esd
The standard uncertainty (estimated standard deviation)
of attribute U[3][3] in category atom_site_anisotrop.
atom_site_anisotrop.pdbx_PDB_ins_code
Pointer to attribute pdbx_PDB_ins_code in category atom_site
atom_site_anisotrop.pdbx_auth_alt_id
Pointer to attribute pdbx_auth_alt_id in category atom_site.
atom_site_anisotrop.pdbx_auth_asym_id
Pointer to attribute auth_asym_id in category atom_site
atom_site_anisotrop.pdbx_auth_atom_id
Pointer to attribute auth_atom_id in category atom_site
atom_site_anisotrop.pdbx_auth_comp_id
Pointer to attribute auth_comp_id in category atom_site
atom_site_anisotrop.pdbx_auth_seq_id
Pointer to attribute auth_seq_id in category atom_site
atom_site_anisotrop.pdbx_label_alt_id
Pointer to attribute label_alt_id in category atom_site.
atom_site_anisotrop.pdbx_label_asym_id
Pointer to attribute label_asym_id in category atom_site
atom_site_anisotrop.pdbx_label_atom_id
Pointer to attribute label_atom_id in category atom_site
atom_site_anisotrop.pdbx_label_comp_id
Pointer to attribute label_comp_id in category atom_site
atom_site_anisotrop.pdbx_label_seq_id
Pointer to attribute label_seq_id in category atom_site
atom_site_anisotrop.ratio
Ratio of the maximum to minimum principal axes of
displacement (thermal) ellipsoids.
atom_site_anisotrop.type_symbol
This data item is a pointer to attribute symbol in category atom_type in the
ATOM_TYPE category.
atom_site_anisotrop.id
This data item is a pointer to attribute id in category atom_site in the ATOM_SITE
category.
atom_sites
Data items in the ATOM_SITES category record details about
the crystallographic cell and cell transformations, which are
common to all atom sites.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:atom_sitesCategory>
<PDBx:atom_sites entry_id="5HVP">
<PDBx:Cartn_transf_matrix11>58.39</PDBx:Cartn_transf_matrix11>
<PDBx:Cartn_transf_matrix12>0.00</PDBx:Cartn_transf_matrix12>
<PDBx:Cartn_transf_matrix13>0.00</PDBx:Cartn_transf_matrix13>
<PDBx:Cartn_transf_matrix21>0.00</PDBx:Cartn_transf_matrix21>
<PDBx:Cartn_transf_matrix22>86.70</PDBx:Cartn_transf_matrix22>
<PDBx:Cartn_transf_matrix23>0.00</PDBx:Cartn_transf_matrix23>
<PDBx:Cartn_transf_matrix31>0.00</PDBx:Cartn_transf_matrix31>
<PDBx:Cartn_transf_matrix32>0.00</PDBx:Cartn_transf_matrix32>
<PDBx:Cartn_transf_matrix33>46.27</PDBx:Cartn_transf_matrix33>
<PDBx:Cartn_transf_vector1>0.00</PDBx:Cartn_transf_vector1>
<PDBx:Cartn_transf_vector2>0.00</PDBx:Cartn_transf_vector2>
<PDBx:Cartn_transf_vector3>0.00</PDBx:Cartn_transf_vector3>
<PDBx:Cartn_transform_axes>c along z, astar along x, b along y</PDBx:Cartn_transform_axes>
</PDBx:atom_sites>
</PDBx:atom_sitesCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
atom_sitesCategory
This property indicates that datablock
has a category element atom_sites.
atom_sitesItem
Abstract Datatype property for atom_sites items.
reference_to_atom_sites
cross-reference to atom_sites
atom_sites.Cartn_transf_matrix11
The [1][1] element of the 3x3 matrix used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute Cartn_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.Cartn_transf_matrix12
The [1][2] element of the 3x3 matrix used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute Cartn_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.Cartn_transf_matrix13
The [1][3] element of the 3x3 matrix used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute Cartn_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.Cartn_transf_matrix21
The [2][1] element of the 3x3 matrix used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute Cartn_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.Cartn_transf_matrix22
The [2][2] element of the 3x3 matrix used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute Cartn_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.Cartn_transf_matrix23
The [2][3] element of the 3x3 matrix used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute Cartn_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.Cartn_transf_matrix31
The [3][1] element of the 3x3 matrix used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute Cartn_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.Cartn_transf_matrix32
The [3][2] element of the 3x3 matrix used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute Cartn_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.Cartn_transf_matrix33
The [3][3] element of the 3x3 matrix used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute Cartn_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.Cartn_transf_vector1
The [1] element of the three-element vector used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The rotation matrix is defined in
attribute Cartn_transf_matrix[][].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.Cartn_transf_vector2
The [2] element of the three-element vector used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The rotation matrix is defined in
attribute Cartn_transf_matrix[][].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.Cartn_transf_vector3
The [3] element of the three-element vector used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The rotation matrix is defined in
attribute Cartn_transf_matrix[][].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.Cartn_transform_axes
A description of the relative alignment of the crystal cell
axes to the Cartesian orthogonal axes as applied in the
transformation matrix attribute Cartn_transf_matrix[][] in category atom_sites.
a parallel to x; b in the plane of y and z
atom_sites.fract_transf_matrix11
The [1][1] element of the 3x3 matrix used to transform Cartesian
coordinates in the ATOM_SITE category to fractional coordinates
in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute fract_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.fract_transf_matrix12
The [1][2] element of the 3x3 matrix used to transform Cartesian
coordinates in the ATOM_SITE category to fractional coordinates
in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute fract_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.fract_transf_matrix13
The [1][3] element of the 3x3 matrix used to transform Cartesian
coordinates in the ATOM_SITE category to fractional coordinates
in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute fract_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.fract_transf_matrix21
The [2][1] element of the 3x3 matrix used to transform Cartesian
coordinates in the ATOM_SITE category to fractional coordinates
in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute fract_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.fract_transf_matrix22
The [2][2] element of the 3x3 matrix used to transform Cartesian
coordinates in the ATOM_SITE category to fractional coordinates
in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute fract_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.fract_transf_matrix23
The [2][3] element of the 3x3 matrix used to transform Cartesian
coordinates in the ATOM_SITE category to fractional coordinates
in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute fract_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.fract_transf_matrix31
The [3][1] element of the 3x3 matrix used to transform Cartesian
coordinates in the ATOM_SITE category to fractional coordinates
in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute fract_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.fract_transf_matrix32
The [3][2] element of the 3x3 matrix used to transform Cartesian
coordinates in the ATOM_SITE category to fractional coordinates
in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute fract_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.fract_transf_matrix33
The [3][3] element of the 3x3 matrix used to transform Cartesian
coordinates in the ATOM_SITE category to fractional coordinates
in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x1 translation is defined in
attribute fract_transf_vector[].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.fract_transf_vector1
The [1] element of the three-element vector used to transform
Cartesian coordinates in the ATOM_SITE category to fractional
coordinates in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x3 rotation is defined in
attribute fract_transf_matrix[][].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.fract_transf_vector2
The [2] element of the three-element vector used to transform
Cartesian coordinates in the ATOM_SITE category to fractional
coordinates in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x3 rotation is defined in
attribute fract_transf_matrix[][].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
atom_sites.fract_transf_vector3
The [3] element of the three-element vector used to transform
Cartesian coordinates in the ATOM_SITE category to fractional
coordinates in the same category. The axial alignments of this
transformation are described in attribute Cartn_transform_axes.
in category atom_sites The 3x3 rotation is defined in
attribute fract_transf_matrix[][].
in category atom_sites
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
difmap
vecmap
heavy
direct
geom
disper
isomor
This code identifies the method used to locate the
hydrogen atoms.
*** This data item would not in general be used in a
macromolecular data block. ***
difmap
vecmap
heavy
direct
geom
disper
isomor
This code identifies the method used to locate the initial
atom sites.
*** This data item would not in general be used in a
macromolecular data block. ***
difmap
vecmap
heavy
direct
geom
disper
isomor
This code identifies the method used to locate the
non-hydrogen-atom sites not found by
attribute solution_primary.
in category atom_sites
*** This data item would not in general be used in a
macromolecular data block. ***
atom_sites.special_details
Additional information about the atomic coordinates not coded
elsewhere in the CIF.
atom_sites.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
atom_sites_alt
Data items in the ATOM_SITES_ALT category record details
about the structural ensembles that should be generated from
atom sites or groups of atom sites that are modelled in
alternative conformations in this data block.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:atom_sites_altCategory>
<PDBx:atom_sites_alt id="1">
<PDBx:details> Atom sites with the alternative ID set to 1 have been
modeled in alternative conformations with respect to atom
sites marked with alternative ID 2. The conformations of
amino-acid side chains and solvent atoms with alternative
ID set to 1 correlate with the conformation of the
inhibitor marked with alternative ID 1. They have been
given an occupancy of 0.58 to match the occupancy assigned
to the inhibitor.</PDBx:details>
</PDBx:atom_sites_alt>
<PDBx:atom_sites_alt id="2">
<PDBx:details> Atom sites with the alternative ID set to 2 have been
modeled in alternative conformations with respect to atom
sites marked with alternative ID 1. The conformations of
amino-acid side chains and solvent atoms with alternative
ID set to 2 correlate with the conformation of the
inhibitor marked with alternative ID 2. They have been
given an occupancy of 0.42 to match the occupancy assigned
to the inhibitor.</PDBx:details>
</PDBx:atom_sites_alt>
<PDBx:atom_sites_alt id="3">
<PDBx:details> Atom sites with the alternative ID set to 3 have been
modeled in alternative conformations with respect to
atoms marked with alternative ID 4. The conformations of
amino-acid side chains and solvent atoms with alternative
ID set to 3 do not correlate with the conformation of the
inhibitor. These atom sites have arbitrarily been given
an occupancy of 0.50.</PDBx:details>
</PDBx:atom_sites_alt>
<PDBx:atom_sites_alt id="4">
<PDBx:details> Atom sites with the alternative ID set to 4 have been
modeled in alternative conformations with respect to
atoms marked with alternative ID 3. The conformations of
amino-acid side chains and solvent atoms with alternative
ID set to 4 do not correlate with the conformation of the
inhibitor. These atom sites have arbitrarily been given
an occupancy of 0.50.</PDBx:details>
</PDBx:atom_sites_alt>
</PDBx:atom_sites_altCategory>
0
1
1
atom_sites_altCategory
This property indicates that datablock
has a category element atom_sites_alt.
atom_sites_altItem
Abstract Datatype property for atom_sites_alt items.
reference_to_atom_sites_alt
cross-reference to atom_sites_alt
atom_sites_alt.details
A description of special aspects of the modelling of atoms in
alternative conformations.
atom_sites_alt.id
The value of attribute id in category atom_sites_alt must uniquely identify
a record in the ATOM_SITES_ALT list.
Note that this item need not be a number; it can be any unique
identifier.
orientation 1
molecule abc
atom_sites_alt_ens
Data items in the ATOM_SITES_ALT_ENS category record details
about the ensemble structure generated from atoms with various
alternative conformation IDs.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:atom_sites_alt_ensCategory>
<PDBx:atom_sites_alt_ens id="Ensemble 1-A">
<PDBx:details> The inhibitor binds to the enzyme in two, roughly twofold
symmetric alternative conformations.
This conformational ensemble includes the more populated
conformation of the inhibitor (ID=1) and the amino-acid
side chains and solvent structure that correlate with this
inhibitor conformation.
Also included are one set (ID=3) of side chains with
alternative conformations when the conformations are not
correlated with the inhibitor conformation.</PDBx:details>
</PDBx:atom_sites_alt_ens>
<PDBx:atom_sites_alt_ens id="Ensemble 1-B">
<PDBx:details> The inhibitor binds to the enzyme in two, roughly twofold
symmetric alternative conformations.
This conformational ensemble includes the more populated
conformation of the inhibitor (ID=1) and the amino-acid
side chains and solvent structure that correlate with
this inhibitor conformation.
Also included are one set (ID=4) of side chains with
alternative conformations when the conformations are not
correlated with the inhibitor conformation.</PDBx:details>
</PDBx:atom_sites_alt_ens>
<PDBx:atom_sites_alt_ens id="Ensemble 2-A">
<PDBx:details> The inhibitor binds to the enzyme in two, roughly twofold
symmetric alternative conformations.
This conformational ensemble includes the less populated
conformation of the inhibitor (ID=2) and the amino-acid
side chains and solvent structure that correlate with this
inhibitor conformation.
Also included are one set (ID=3) of side chains with
alternative conformations when the conformations are not
correlated with the inhibitor conformation.</PDBx:details>
</PDBx:atom_sites_alt_ens>
<PDBx:atom_sites_alt_ens id="Ensemble 2-B">
<PDBx:details> The inhibitor binds to the enzyme in two, roughly twofold
symmetric alternative conformations.
This conformational ensemble includes the less populated
conformation of the inhibitor (ID=2) and the amino-acid
side chains and solvent structure that correlate with this
inhibitor conformation.
Also included are one set (ID=4) of side chains with
alternative conformations when the conformations are not
correlated with the inhibitor conformation.</PDBx:details>
</PDBx:atom_sites_alt_ens>
</PDBx:atom_sites_alt_ensCategory>
0
1
1
atom_sites_alt_ensCategory
This property indicates that datablock
has a category element atom_sites_alt_ens.
atom_sites_alt_ensItem
Abstract Datatype property for atom_sites_alt_ens items.
reference_to_atom_sites_alt_ens
cross-reference to atom_sites_alt_ens
atom_sites_alt_ens.details
A description of special aspects of the ensemble structure
generated from atoms with various alternative IDs.
atom_sites_alt_ens.id
The value of attribute id in category atom_sites_alt_ens must uniquely identify a
record in the ATOM_SITES_ALT_ENS list.
Note that this item need not be a number; it can be any unique
identifier.
atom_sites_alt_gen
Data items in the ATOM_SITES_ALT_GEN category record details
about the interpretation of multiple conformations in the
structure.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:atom_sites_alt_genCategory>
<PDBx:atom_sites_alt_gen alt_id="1" ens_id="Ensemble 1-A"></PDBx:atom_sites_alt_gen>
<PDBx:atom_sites_alt_gen alt_id="2" ens_id="Ensemble 1-A"></PDBx:atom_sites_alt_gen>
<PDBx:atom_sites_alt_gen alt_id="1" ens_id="Ensemble 1-B"></PDBx:atom_sites_alt_gen>
<PDBx:atom_sites_alt_gen alt_id="4" ens_id="Ensemble 1-B"></PDBx:atom_sites_alt_gen>
<PDBx:atom_sites_alt_gen alt_id="2" ens_id="Ensemble 2-A"></PDBx:atom_sites_alt_gen>
<PDBx:atom_sites_alt_gen alt_id="3" ens_id="Ensemble 2-A"></PDBx:atom_sites_alt_gen>
<PDBx:atom_sites_alt_gen alt_id="2" ens_id="Ensemble 2-B"></PDBx:atom_sites_alt_gen>
<PDBx:atom_sites_alt_gen alt_id="4" ens_id="Ensemble 2-B"></PDBx:atom_sites_alt_gen>
</PDBx:atom_sites_alt_genCategory>
1
1
atom_sites_alt_genCategory
This property indicates that datablock
has a category element atom_sites_alt_gen.
atom_sites_alt_genItem
Abstract Datatype property for atom_sites_alt_gen items.
reference_to_atom_sites_alt_gen
cross-reference to atom_sites_alt_gen
atom_sites_alt_gen.alt_id
This data item is a pointer to attribute id in category atom_sites_alt in the
ATOM_SITES_ALT category.
atom_sites_alt_gen.ens_id
This data item is a pointer to attribute id in category atom_sites_alt_ens in the
ATOM_SITES_ALT_ENS category.
atom_sites_footnote
Data items in the ATOM_SITES_FOOTNOTE category record detailed
comments about an atom site or a group of atom sites.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:atom_sites_footnoteCategory>
<PDBx:atom_sites_footnote id="1">
<PDBx:text> The inhibitor binds to the enzyme in two alternative
orientations. The two orientations have been assigned
alternative IDs *1* and *2*.</PDBx:text>
</PDBx:atom_sites_footnote>
<PDBx:atom_sites_footnote id="2">
<PDBx:text> Side chains of these residues adopt alternative
orientations that correlate with the alternative
orientations of the inhibitor.
Side chains with alternative ID *1* and occupancy 0.58
correlate with inhibitor orientation *1*.
Side chains with alternative ID *2* and occupancy 0.42
correlate with inhibitor orientation *2*.</PDBx:text>
</PDBx:atom_sites_footnote>
<PDBx:atom_sites_footnote id="3">
<PDBx:text> The positions of these water molecules correlate with
the alternative orientations of the inhibitor.
Water molecules with alternative ID *1* and occupancy 0.58
correlate with inhibitor orientation *1*.
Water molecules with alternative ID *2* and occupancy 0.42
correlate with inhibitor orientation *2*.</PDBx:text>
</PDBx:atom_sites_footnote>
<PDBx:atom_sites_footnote id="4">
<PDBx:text> Side chains of these residues adopt alternative
orientations that do not correlate with the alternative
orientation of the inhibitor.</PDBx:text>
</PDBx:atom_sites_footnote>
<PDBx:atom_sites_footnote id="5">
<PDBx:text> The positions of these water molecules correlate with
alternative orientations of amino-acid side chains that
do not correlate with alternative orientations of the
inhibitor.</PDBx:text>
</PDBx:atom_sites_footnote>
</PDBx:atom_sites_footnoteCategory>
0
1
1
atom_sites_footnoteCategory
This property indicates that datablock
has a category element atom_sites_footnote.
atom_sites_footnoteItem
Abstract Datatype property for atom_sites_footnote items.
reference_to_atom_sites_footnote
cross-reference to atom_sites_footnote
atom_sites_footnote.text
The text of the footnote. Footnotes are used to describe
an atom site or a group of atom sites in the ATOM_SITE list.
For example, footnotes may be used to indicate atoms for which
the electron density is very weak, or atoms for which static
disorder has been modelled.
atom_sites_footnote.id
A code that identifies the footnote.
a
b
1
2
atom_type
Data items in the ATOM_TYPE category record details about the
properties of the atoms that occupy the atom sites, such as the
atomic scattering factors.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:atom_typeCategory>
<PDBx:atom_type symbol="C">
<PDBx:oxidation_number>0</PDBx:oxidation_number>
<PDBx:scat_Cromer_Mann_a1>2.31000</PDBx:scat_Cromer_Mann_a1>
<PDBx:scat_Cromer_Mann_a2>20.8439</PDBx:scat_Cromer_Mann_a2>
<PDBx:scat_Cromer_Mann_a3>1.02000</PDBx:scat_Cromer_Mann_a3>
<PDBx:scat_Cromer_Mann_a4>10.2075</PDBx:scat_Cromer_Mann_a4>
<PDBx:scat_Cromer_Mann_b1>1.58860</PDBx:scat_Cromer_Mann_b1>
<PDBx:scat_Cromer_Mann_b2>0.568700</PDBx:scat_Cromer_Mann_b2>
<PDBx:scat_Cromer_Mann_b3>0.865000</PDBx:scat_Cromer_Mann_b3>
<PDBx:scat_Cromer_Mann_b4>51.6512</PDBx:scat_Cromer_Mann_b4>
<PDBx:scat_Cromer_Mann_c>0.21560</PDBx:scat_Cromer_Mann_c>
</PDBx:atom_type>
<PDBx:atom_type symbol="N">
<PDBx:oxidation_number>0</PDBx:oxidation_number>
<PDBx:scat_Cromer_Mann_a1>12.2126</PDBx:scat_Cromer_Mann_a1>
<PDBx:scat_Cromer_Mann_a2>0.005700</PDBx:scat_Cromer_Mann_a2>
<PDBx:scat_Cromer_Mann_a3>3.13220</PDBx:scat_Cromer_Mann_a3>
<PDBx:scat_Cromer_Mann_a4>9.89330</PDBx:scat_Cromer_Mann_a4>
<PDBx:scat_Cromer_Mann_b1>2.01250</PDBx:scat_Cromer_Mann_b1>
<PDBx:scat_Cromer_Mann_b2>28.9975</PDBx:scat_Cromer_Mann_b2>
<PDBx:scat_Cromer_Mann_b3>1.16630</PDBx:scat_Cromer_Mann_b3>
<PDBx:scat_Cromer_Mann_b4>0.582600</PDBx:scat_Cromer_Mann_b4>
<PDBx:scat_Cromer_Mann_c>-11.529</PDBx:scat_Cromer_Mann_c>
</PDBx:atom_type>
<PDBx:atom_type symbol="O">
<PDBx:oxidation_number>0</PDBx:oxidation_number>
<PDBx:scat_Cromer_Mann_a1>3.04850</PDBx:scat_Cromer_Mann_a1>
<PDBx:scat_Cromer_Mann_a2>13.2771</PDBx:scat_Cromer_Mann_a2>
<PDBx:scat_Cromer_Mann_a3>2.28680</PDBx:scat_Cromer_Mann_a3>
<PDBx:scat_Cromer_Mann_a4>5.70110</PDBx:scat_Cromer_Mann_a4>
<PDBx:scat_Cromer_Mann_b1>1.54630</PDBx:scat_Cromer_Mann_b1>
<PDBx:scat_Cromer_Mann_b2>0.323900</PDBx:scat_Cromer_Mann_b2>
<PDBx:scat_Cromer_Mann_b3>0.867000</PDBx:scat_Cromer_Mann_b3>
<PDBx:scat_Cromer_Mann_b4>32.9089</PDBx:scat_Cromer_Mann_b4>
<PDBx:scat_Cromer_Mann_c>0.250800</PDBx:scat_Cromer_Mann_c>
</PDBx:atom_type>
<PDBx:atom_type symbol="S">
<PDBx:oxidation_number>0</PDBx:oxidation_number>
<PDBx:scat_Cromer_Mann_a1>6.90530</PDBx:scat_Cromer_Mann_a1>
<PDBx:scat_Cromer_Mann_a2>1.46790</PDBx:scat_Cromer_Mann_a2>
<PDBx:scat_Cromer_Mann_a3>5.20340</PDBx:scat_Cromer_Mann_a3>
<PDBx:scat_Cromer_Mann_a4>22.2151</PDBx:scat_Cromer_Mann_a4>
<PDBx:scat_Cromer_Mann_b1>1.43790</PDBx:scat_Cromer_Mann_b1>
<PDBx:scat_Cromer_Mann_b2>0.253600</PDBx:scat_Cromer_Mann_b2>
<PDBx:scat_Cromer_Mann_b3>1.58630</PDBx:scat_Cromer_Mann_b3>
<PDBx:scat_Cromer_Mann_b4>56.1720</PDBx:scat_Cromer_Mann_b4>
<PDBx:scat_Cromer_Mann_c>0.866900</PDBx:scat_Cromer_Mann_c>
</PDBx:atom_type>
<PDBx:atom_type symbol="CL">
<PDBx:oxidation_number>-1</PDBx:oxidation_number>
<PDBx:scat_Cromer_Mann_a1>18.2915</PDBx:scat_Cromer_Mann_a1>
<PDBx:scat_Cromer_Mann_a2>0.006600</PDBx:scat_Cromer_Mann_a2>
<PDBx:scat_Cromer_Mann_a3>7.20840</PDBx:scat_Cromer_Mann_a3>
<PDBx:scat_Cromer_Mann_a4>1.17170</PDBx:scat_Cromer_Mann_a4>
<PDBx:scat_Cromer_Mann_b1>6.53370</PDBx:scat_Cromer_Mann_b1>
<PDBx:scat_Cromer_Mann_b2>19.5424</PDBx:scat_Cromer_Mann_b2>
<PDBx:scat_Cromer_Mann_b3>2.33860</PDBx:scat_Cromer_Mann_b3>
<PDBx:scat_Cromer_Mann_b4>60.4486</PDBx:scat_Cromer_Mann_b4>
<PDBx:scat_Cromer_Mann_c>-16.378</PDBx:scat_Cromer_Mann_c>
</PDBx:atom_type>
</PDBx:atom_typeCategory>
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<PDBx:atom_typeCategory>
<PDBx:atom_type symbol="C">
<PDBx:number_in_cell>72</PDBx:number_in_cell>
<PDBx:oxidation_number>0</PDBx:oxidation_number>
<PDBx:scat_dispersion_imag>.009</PDBx:scat_dispersion_imag>
<PDBx:scat_dispersion_real>.017</PDBx:scat_dispersion_real>
<PDBx:scat_source>International_Tables_Vol_IV_Table_2.2B</PDBx:scat_source>
</PDBx:atom_type>
<PDBx:atom_type symbol="H">
<PDBx:number_in_cell>100</PDBx:number_in_cell>
<PDBx:oxidation_number>0</PDBx:oxidation_number>
<PDBx:scat_dispersion_imag>0</PDBx:scat_dispersion_imag>
<PDBx:scat_dispersion_real>0</PDBx:scat_dispersion_real>
<PDBx:scat_source>International_Tables_Vol_IV_Table_2.2B</PDBx:scat_source>
</PDBx:atom_type>
<PDBx:atom_type symbol="O">
<PDBx:number_in_cell>12</PDBx:number_in_cell>
<PDBx:oxidation_number>0</PDBx:oxidation_number>
<PDBx:scat_dispersion_imag>.032</PDBx:scat_dispersion_imag>
<PDBx:scat_dispersion_real>.047</PDBx:scat_dispersion_real>
<PDBx:scat_source>International_Tables_Vol_IV_Table_2.2B</PDBx:scat_source>
</PDBx:atom_type>
<PDBx:atom_type symbol="N">
<PDBx:number_in_cell>4</PDBx:number_in_cell>
<PDBx:oxidation_number>0</PDBx:oxidation_number>
<PDBx:scat_dispersion_imag>.018</PDBx:scat_dispersion_imag>
<PDBx:scat_dispersion_real>.029</PDBx:scat_dispersion_real>
<PDBx:scat_source>International_Tables_Vol_IV_Table_2.2B</PDBx:scat_source>
</PDBx:atom_type>
</PDBx:atom_typeCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
atom_typeCategory
This property indicates that datablock
has a category element atom_type.
atom_typeItem
Abstract Datatype property for atom_type items.
reference_to_atom_type
cross-reference to atom_type
atom_type.analytical_mass_percent
Mass percentage of this atom type derived from chemical analysis.
atom_type.description
A description of the atom(s) designated by this atom type. In
most cases, this is the element name and oxidation state of
a single atom species. For disordered or nonstoichiometric
structures it will describe a combination of atom species.
deuterium
0.34Fe+0.66Ni
atom_type.number_in_cell
Total number of atoms of this atom type in the unit cell.
atom_type.oxidation_number
Formal oxidation state of this atom type in the structure.
atom_type.radius_bond
The effective intramolecular bonding radius in angstroms
of this atom type.
atom_type.radius_contact
The effective intermolecular bonding radius in angstroms
of this atom type.
atom_type.scat_Cromer_Mann_a1
The Cromer-Mann scattering-factor coefficient a1 used to
calculate the scattering factors for this atom type.
Ref: International Tables for X-ray Crystallography (1974).
Vol. IV, Table 2.2B
or: International Tables for Crystallography (2004). Vol. C,
Tables 6.1.1.4 and 6.1.1.5.
atom_type.scat_Cromer_Mann_a2
The Cromer-Mann scattering-factor coefficient a2 used to
calculate the scattering factors for this atom type.
Ref: International Tables for X-ray Crystallography (1974).
Vol. IV, Table 2.2B
or: International Tables for Crystallography (2004). Vol. C,
Tables 6.1.1.4 and 6.1.1.5.
atom_type.scat_Cromer_Mann_a3
The Cromer-Mann scattering-factor coefficient a3 used to
calculate the scattering factors for this atom type.
Ref: International Tables for X-ray Crystallography (1974).
Vol. IV, Table 2.2B
or: International Tables for Crystallography (2004). Vol. C,
Tables 6.1.1.4 and 6.1.1.5.
atom_type.scat_Cromer_Mann_a4
The Cromer-Mann scattering-factor coefficient a4 used to
calculate the scattering factors for this atom type.
Ref: International Tables for X-ray Crystallography (1974).
Vol. IV, Table 2.2B
or: International Tables for Crystallography (2004). Vol. C,
Tables 6.1.1.4 and 6.1.1.5.
atom_type.scat_Cromer_Mann_b1
The Cromer-Mann scattering-factor coefficient b1 used to
calculate the scattering factors for this atom type.
Ref: International Tables for X-ray Crystallography (1974).
Vol. IV, Table 2.2B
or: International Tables for Crystallography (2004). Vol. C,
Tables 6.1.1.4 and 6.1.1.5.
atom_type.scat_Cromer_Mann_b2
The Cromer-Mann scattering-factor coefficient b2 used to
calculate the scattering factors for this atom type.
Ref: International Tables for X-ray Crystallography (1974).
Vol. IV, Table 2.2B
or: International Tables for Crystallography (2004). Vol. C,
Tables 6.1.1.4 and 6.1.1.5.
atom_type.scat_Cromer_Mann_b3
The Cromer-Mann scattering-factor coefficient b3 used to
calculate the scattering factors for this atom type.
Ref: International Tables for X-ray Crystallography (1974).
Vol. IV, Table 2.2B
or: International Tables for Crystallography (2004). Vol. C,
Tables 6.1.1.4 and 6.1.1.5.
atom_type.scat_Cromer_Mann_b4
The Cromer-Mann scattering-factor coefficient b4 used to
calculate the scattering factors for this atom type.
Ref: International Tables for X-ray Crystallography (1974).
Vol. IV, Table 2.2B
or: International Tables for Crystallography (2004). Vol. C,
Tables 6.1.1.4 and 6.1.1.5.
atom_type.scat_Cromer_Mann_c
The Cromer-Mann scattering-factor coefficient c used to
calculate the scattering factors for this atom type.
Ref: International Tables for X-ray Crystallography (1974).
Vol. IV, Table 2.2B
or: International Tables for Crystallography (2004). Vol. C,
Tables 6.1.1.4 and 6.1.1.5.
atom_type.scat_dispersion_imag
The imaginary component of the anomalous-dispersion
scattering factor, f'', in electrons for this atom type and
the radiation identified by attribute id in category diffrn_radiation_wavelength.
atom_type.scat_dispersion_real
The real component of the anomalous-dispersion
scattering factor, f', in electrons for this atom type and
the radiation identified by attribute id in category diffrn_radiation_wavelength.
atom_type.scat_dispersion_source
Reference to the source of the real and imaginary dispersion
corrections for scattering factors used for this atom type.
International Tables Vol. IV Table 2.3.1
atom_type.scat_length_neutron
The bound coherent scattering length in femtometres for the
atom type at the isotopic composition used for the diffraction
experiment.
atom_type.scat_source
Reference to the source of the scattering factors or scattering
lengths used for this atom type.
International Tables Vol. IV Table 2.4.6B
atom_type.scat_versus_stol_list
A table of scattering factors as a function of sin theta over
lambda. This table should be well commented to indicate the
items present. Regularly formatted lists are strongly
recommended.
atom_type.symbol
The code used to identify the atom species (singular or plural)
representing this atom type. Normally this code is the element
symbol. The code may be composed of any character except
an underscore with the additional proviso that digits designate
an oxidation state and must be followed by a + or - character.
C
Cu2+
H(SDS)
dummy
FeNi
audit
Data items in the AUDIT category record details about the
creation and subsequent updating of the data block.
Note that these items apply only to the creation and updating of
the data block, and should not be confused with the data items
in the JOURNAL category that record different stages in the
publication of the material in the data block.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:auditCategory>
<PDBx:audit revision_id="1">
<PDBx:creation_date>1992-12-08</PDBx:creation_date>
<PDBx:creation_method> Created by hand from PDB entry 5HVP, from the J. Biol.
Chem. paper describing this structure and from
laboratory records</PDBx:creation_method>
<PDBx:update_record> 1992-12-09 adjusted to reflect comments from B. McKeever
1992-12-10 adjusted to reflect comments from H. Berman
1992-12-12 adjusted to reflect comments from K. Watenpaugh</PDBx:update_record>
</PDBx:audit>
</PDBx:auditCategory>
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<PDBx:auditCategory>
<PDBx:audit revision_id="2">
<PDBx:creation_date>1991-03-20</PDBx:creation_date>
<PDBx:creation_method>from_xtal_archive_file_using_CIFIO</PDBx:creation_method>
<PDBx:update_record> 1991-04-09 text and data added by Tony Willis.
1991-04-15 rec'd by co-editor as manuscript HL0007.
1991-04-17 adjustments based on first referee report.
1991-04-18 adjustments based on second referee report.</PDBx:update_record>
</PDBx:audit>
</PDBx:auditCategory>
0
1
0
1
0
1
1
auditCategory
This property indicates that datablock
has a category element audit.
auditItem
Abstract Datatype property for audit items.
reference_to_audit
cross-reference to audit
audit.creation_date
A date that the data block was created. The date format is
yyyy-mm-dd.
1990-07-12
audit.creation_method
A description of how data were entered into the data block.
spawned by the program QBEE
audit.update_record
A record of any changes to the data block. The update format is
a date (yyyy-mm-dd) followed by a description of the changes.
The latest update entry is added to the bottom of this record.
1990-07-15 Updated by the Co-editor
audit.revision_id
The value of attribute revision_id in category audit must uniquely identify a record
in the AUDIT list.
rev1
audit_author
Data items in the AUDIT_AUTHOR category record details about
the author(s) of the data block.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:audit_authorCategory>
<PDBx:audit_author pdbx_ordinal="1">
<PDBx:address> Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA</PDBx:address>
<PDBx:name>Fitzgerald, Paula M.D.</PDBx:name>
</PDBx:audit_author>
<PDBx:audit_author pdbx_ordinal="2">
<PDBx:address> Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA</PDBx:address>
<PDBx:name>McKeever, Brian M.</PDBx:name>
</PDBx:audit_author>
<PDBx:audit_author pdbx_ordinal="3">
<PDBx:address> Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA</PDBx:address>
<PDBx:name>Van Middlesworth, J.F.</PDBx:name>
</PDBx:audit_author>
<PDBx:audit_author pdbx_ordinal="4">
<PDBx:address> Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA</PDBx:address>
<PDBx:name>Springer, James P.</PDBx:name>
</PDBx:audit_author>
</PDBx:audit_authorCategory>
0
1
1
1
1
audit_authorCategory
This property indicates that datablock
has a category element audit_author.
audit_authorItem
Abstract Datatype property for audit_author items.
reference_to_audit_author
cross-reference to audit_author
audit_author.address
The address of an author of this data block. If there are
multiple authors, attribute address in category audit_author is looped with
attribute name in category audit_author.
Department
Institute
Street
City and postcode
COUNTRY
audit_author.name
The name of an author of this data block. If there are multiple
authors, _audit_author.name is looped with _audit_author.address.
The family name(s), followed by a comma and including any
dynastic components, precedes the first name(s) or initial(s).
Bleary, Percival R.
O'Neil, F.K.
Van den Bossche, G.
Yang, D.-L.
Simonov, Yu.A
audit_author.pdbx_ordinal
This data item defines the order of the author's name in the
list of audit authors.
1
2
3
audit_conform
Data items in the AUDIT_CONFORM category describe the
dictionary versions against which the data names appearing in
the current data block are conformant.
Example 1 - any file conforming to the current CIF core dictionary.
<PDBx:audit_conformCategory>
<PDBx:audit_conform dict_name="cif_core.dic" dict_version="2.3.1">
<PDBx:dict_location>ftp://ftp.iucr.org/pub/cif_core.2.3.1.dic</PDBx:dict_location>
</PDBx:audit_conform>
</PDBx:audit_conformCategory>
0
1
1
1
audit_conformCategory
This property indicates that datablock
has a category element audit_conform.
audit_conformItem
Abstract Datatype property for audit_conform items.
reference_to_audit_conform
cross-reference to audit_conform
audit_conform.dict_location
A file name or uniform resource locator (URL) for the
dictionary to which the current data block conforms.
audit_conform.dict_name
The string identifying the highest-level dictionary defining
data names used in this file.
audit_conform.dict_version
The version number of the dictionary to which the current
data block conforms.
audit_contact_author
Data items in the AUDIT_CONTACT_AUTHOR category record details
about the name and address of the author to be contacted
concerning the content of this data block.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:audit_contact_authorCategory>
<PDBx:audit_contact_author name="Fitzgerald, Paula M.D.">
<PDBx:address> Department of Biophysical Chemistry
Merck Research Laboratories
PO Box 2000, Ry80M203
Rahway, New Jersey 07065
USA</PDBx:address>
<PDBx:email>paula_fitzgerald@merck.com</PDBx:email>
<PDBx:fax>1(908)5946645</PDBx:fax>
<PDBx:phone>1(908)5945510</PDBx:phone>
</PDBx:audit_contact_author>
</PDBx:audit_contact_authorCategory>
0
1
0
1
0
1
0
1
1
audit_contact_authorCategory
This property indicates that datablock
has a category element audit_contact_author.
audit_contact_authorItem
Abstract Datatype property for audit_contact_author items.
reference_to_audit_contact_author
cross-reference to audit_contact_author
audit_contact_author.address
The mailing address of the author of the data block to whom
correspondence should be addressed.
Department
Institute
Street
City and postcode
COUNTRY
audit_contact_author.email
The electronic mail address of the author of the data block to
whom correspondence should be addressed, in a form recognizable
to international networks. The format of e-mail
addresses is given in Section 3.4, Address Specification, of
Internet Message Format, RFC 2822, P. Resnick (Editor),
Network Standards Group, April 2001.
name@host.domain.country
bm@iucr.org
audit_contact_author.fax
The facsimile telephone number of the author of the data
block to whom correspondence should be addressed.
The recommended style starts with the international dialing
prefix, followed by the area code in parentheses, followed by the
local number with no spaces.
12(34)9477334
12()349477334
audit_contact_author.phone
The telephone number of the author of the data block to whom
correspondence should be addressed.
The recommended style starts with the international dialing
prefix, followed by the area code in parentheses, followed by the
local number and any extension number prefixed by 'x',
with no spaces.
12(34)9477330
12()349477330
12(34)9477330x5543
audit_contact_author.name
The name of the author of the data block to whom correspondence
should be addressed.
The family name(s), followed by a comma and including any
dynastic components, precedes the first name(s) or initial(s).
Bleary, Percival R.
O'Neil, F.K.
Van den Bossche, G.
Yang, D.-L.
Simonov, Yu.A
audit_link
Data items in the AUDIT_LINK category record details about the
relationships between data blocks in the current CIF.
Example 1 - multiple structure paper, as illustrated
in A Guide to CIF for Authors (1995). IUCr: Chester.
<PDBx:audit_linkCategory>
<PDBx:audit_link block_code="morA_pub" block_description="discursive text of paper with two structures"></PDBx:audit_link>
<PDBx:audit_link block_code="morA_(1)" block_description="structure 1 of 2"></PDBx:audit_link>
<PDBx:audit_link block_code="morA_(2)" block_description="structure 2 of 2"></PDBx:audit_link>
</PDBx:audit_linkCategory>
Example 2 - example file for the one-dimensional incommensurately
modulated structure of K~2~SeO~4~.
<PDBx:audit_linkCategory>
<PDBx:audit_link block_code="KSE_PUB" block_description="publication details"></PDBx:audit_link>
<PDBx:audit_link block_code="KSE_COM" block_description="experimental data common to ref./mod. structures"></PDBx:audit_link>
<PDBx:audit_link block_code="KSE_REF" block_description="reference structure"></PDBx:audit_link>
<PDBx:audit_link block_code="KSE_MOD" block_description="modulated structure"></PDBx:audit_link>
</PDBx:audit_linkCategory>
1
1
audit_linkCategory
This property indicates that datablock
has a category element audit_link.
audit_linkItem
Abstract Datatype property for audit_link items.
reference_to_audit_link
cross-reference to audit_link
audit_link.block_code
The value of attribute code in category audit_block associated with a data block
in the current file related to the current data block. The
special value '.' may be used to refer to the current data
block for completeness.
audit_link.block_description
A textual description of the relationship of the referenced
data block to the current one.
cell
Data items in the CELL category record details about the
crystallographic cell parameters.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:cellCategory>
<PDBx:cell entry_id="5HVP">
<PDBx:angle_alpha>90.00</PDBx:angle_alpha>
<PDBx:angle_beta>90.00</PDBx:angle_beta>
<PDBx:angle_gamma>90.00</PDBx:angle_gamma>
<PDBx:details> The cell parameters were refined every twenty frames during
data integration. The cell lengths given are the mean of
55 such refinements; the esds given are the root mean
square deviations of these 55 observations from that mean.</PDBx:details>
<PDBx:length_a>58.39</PDBx:length_a>
<PDBx:length_a_esd>0.05</PDBx:length_a_esd>
<PDBx:length_b>86.70</PDBx:length_b>
<PDBx:length_b_esd>0.12</PDBx:length_b_esd>
<PDBx:length_c>46.27</PDBx:length_c>
<PDBx:length_c_esd>0.06</PDBx:length_c_esd>
<PDBx:volume>234237</PDBx:volume>
</PDBx:cell>
</PDBx:cellCategory>
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<PDBx:cellCategory>
<PDBx:cell entry_id="1TOZ">
<PDBx:angle_alpha>90.0</PDBx:angle_alpha>
<PDBx:angle_beta>90.0</PDBx:angle_beta>
<PDBx:angle_gamma>90.0</PDBx:angle_gamma>
<PDBx:length_a>5.959</PDBx:length_a>
<PDBx:length_a_esd>0.001</PDBx:length_a_esd>
<PDBx:length_b>14.956</PDBx:length_b>
<PDBx:length_b_esd>0.001</PDBx:length_b_esd>
<PDBx:length_c>19.737</PDBx:length_c>
<PDBx:length_c_esd>0.003</PDBx:length_c_esd>
<PDBx:volume>1759.0</PDBx:volume>
<PDBx:volume_esd>0.3</PDBx:volume_esd>
</PDBx:cell>
</PDBx:cellCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
cellCategory
This property indicates that datablock
has a category element cell.
cellItem
Abstract Datatype property for cell items.
reference_to_cell
cross-reference to cell
cell.Z_PDB
The number of the polymeric chains in a unit cell. In the case
of heteropolymers, Z is the number of occurrences of the most
populous chain.
This data item is provided for compatibility with the original
Protein Data Bank format, and only for that purpose.
cell.angle_alpha
Unit-cell angle alpha of the reported structure in degrees.
cell.angle_alpha_esd
The standard uncertainty (estimated standard deviation)
of attribute angle_alpha in category cell.
cell.angle_beta
Unit-cell angle beta of the reported structure in degrees.
cell.angle_beta_esd
The standard uncertainty (estimated standard deviation)
of attribute angle_beta in category cell.
cell.angle_gamma
Unit-cell angle gamma of the reported structure in degrees.
cell.angle_gamma_esd
The standard uncertainty (estimated standard deviation)
of attribute angle_gamma in category cell.
cell.details
A description of special aspects of the cell choice, noting
possible alternative settings.
pseudo-orthorhombic
standard setting from 45 deg rotation around c
cell.formula_units_Z
The number of the formula units in the unit cell as specified
by _chemical_formula.structural, _chemical_formula.moiety or
attribute sum in category chemical_formula.
cell.length_a
Unit-cell length a corresponding to the structure reported in
angstroms.
cell.length_a_esd
The standard uncertainty (estimated standard deviation)
of attribute length_a in category cell.
cell.length_b
Unit-cell length b corresponding to the structure reported in
angstroms.
cell.length_b_esd
The standard uncertainty (estimated standard deviation)
of attribute length_b in category cell.
cell.length_c
Unit-cell length c corresponding to the structure reported in
angstroms.
cell.length_c_esd
The standard uncertainty (estimated standard deviation)
of attribute length_c in category cell.
cell.pdbx_unique_axis
To further identify unique axis if necessary. E.g., P 21 with
an unique C axis will have 'C' in this field.
cell.reciprocal_angle_alpha
The angle (recip-alpha) defining the reciprocal cell in degrees.
(recip-alpha), (recip-alpha) and (recip-alpha) related to the
angles in the real cell by:
cos(recip-alpha)
= [cos(beta)*cos(gamma) - cos(alpha)]/[sin(beta)*sin(gamma)]
cos(recip-beta)
= [cos(gamma)*cos(alpha) - cos(beta)]/[sin(gamma)*sin(alpha)]
cos(recip-gamma)
= [cos(alpha)*cos(beta) - cos(gamma)]/[sin(alpha)*sin(beta)]
Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360.
New York: John Wiley & Sons Inc.
cell.reciprocal_angle_alpha_esd
The estimated standard deviation of attribute reciprocal_angle_alpha in category cell.
cell.reciprocal_angle_beta
The angle (recip-beta) defining the reciprocal cell in degrees.
(recip-alpha), (recip-alpha) and (recip-alpha) related to the
angles in the real cell by:
cos(recip-alpha)
= [cos(beta)*cos(gamma) - cos(alpha)]/[sin(beta)*sin(gamma)]
cos(recip-beta)
= [cos(gamma)*cos(alpha) - cos(beta)]/[sin(gamma)*sin(alpha)]
cos(recip-gamma)
= [cos(alpha)*cos(beta) - cos(gamma)]/[sin(alpha)*sin(beta)]
Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360.
New York: John Wiley & Sons Inc.
cell.reciprocal_angle_beta_esd
The estimated standard deviation of attribute reciprocal_angle_beta in category cell.
cell.reciprocal_angle_gamma
The angle (recip-gamma) defining the reciprocal cell in degrees.
(recip-alpha), (recip-alpha) and (recip-alpha) related to the
angles in the real cell by:
cos(recip-alpha)
= [cos(beta)*cos(gamma) - cos(alpha)]/[sin(beta)*sin(gamma)]
cos(recip-beta)
= [cos(gamma)*cos(alpha) - cos(beta)]/[sin(gamma)*sin(alpha)]
cos(recip-gamma)
= [cos(alpha)*cos(beta) - cos(gamma)]/[sin(alpha)*sin(beta)]
Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360.
New York: John Wiley & Sons Inc.
cell.reciprocal_angle_gamma_esd
The estimated standard deviation of attribute reciprocal_angle_gamma in category cell.
cell.reciprocal_length_a
The reciprocal cell length (recip-a) in inverse Angstroms.
(recip-a), (recip-b) and (recip-c) are related to the real cell
by the following equation:
recip-a = b*c*sin(alpha)/V
recip-b = c*a*sin(beta)/V
recip-c = a*b*sin(gamma)/V
where V is the cell volume.
Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360.
New York: John Wiley & Sons Inc.
cell.reciprocal_length_a_esd
The estimated standard deviation of attribute reciprocal_length_a in category cell.
cell.reciprocal_length_b
The reciprocal cell length (recip-b) in inverse Angstroms.
(recip-a), (recip-b) and (recip-c) are related to the real cell
by the following equation:
recip-a = b*c*sin(alpha)/V
recip-b = c*a*sin(beta)/V
recip-c = a*b*sin(gamma)/V
where V is the cell volume.
Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360.
New York: John Wiley & Sons Inc.
cell.reciprocal_length_b_esd
The estimated standard deviation of attribute reciprocal_length_b in category cell.
cell.reciprocal_length_c
The reciprocal cell length (recip-c) in inverse Angstroms.
(recip-a), (recip-b) and (recip-c) are related to the real cell
by the following equation:
recip-a = b*c*sin(alpha)/V
recip-b = c*a*sin(beta)/V
recip-c = a*b*sin(gamma)/V
where V is the cell volume.
Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360.
New York: John Wiley & Sons Inc.
cell.reciprocal_length_c_esd
The estimated standard deviation of attribute reciprocal_length_c in category cell.
cell.volume
Cell volume V in angstroms cubed.
V = a b c (1 - cos^2^~alpha~ - cos^2^~beta~ - cos^2^~gamma~
+ 2 cos~alpha~ cos~beta~ cos~gamma~)^1/2^
a = attribute length_a
in category cell b = attribute length_b
in category cell c = attribute length_c
in category cell alpha = attribute angle_alpha
in category cell beta = attribute angle_beta
in category cell gamma = attribute angle_gamma in category cell
cell.volume_esd
The standard uncertainty (estimated standard deviation)
of attribute volume in category cell.
cell.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
cell_measurement
Data items in the CELL_MEASUREMENT category record details
about the measurement of the crystallographic cell parameters.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:cell_measurementCategory>
<PDBx:cell_measurement entry_id="5HVP">
<PDBx:temp>293</PDBx:temp>
<PDBx:temp_esd>3</PDBx:temp_esd>
<PDBx:theta_max>31</PDBx:theta_max>
<PDBx:theta_min>11</PDBx:theta_min>
<PDBx:wavelength>1.54</PDBx:wavelength>
</PDBx:cell_measurement>
</PDBx:cell_measurementCategory>
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<PDBx:cell_measurementCategory>
<PDBx:cell_measurement entry_id="1TOZ">
<PDBx:reflns_used>25</PDBx:reflns_used>
<PDBx:temp>293</PDBx:temp>
<PDBx:theta_max>31</PDBx:theta_max>
<PDBx:theta_min>25</PDBx:theta_min>
</PDBx:cell_measurement>
</PDBx:cell_measurementCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
cell_measurementCategory
This property indicates that datablock
has a category element cell_measurement.
cell_measurementItem
Abstract Datatype property for cell_measurement items.
reference_to_cell_measurement
cross-reference to cell_measurement
cell_measurement.pressure
The pressure in kilopascals at which the unit-cell parameters
were measured (not the pressure at which the sample was
synthesized).
cell_measurement.pressure_esd
The standard uncertainty (estimated standard deviation)
of attribute pressure in category cell_measurement.
cell_measurement.radiation
Description of the radiation used to measure the unit-cell data.
See also attribute wavelength in category cell_measurement.
neutron
Cu K\a
synchrotron
cell_measurement.reflns_used
The total number of reflections used to determine the unit cell.
These reflections may be specified as CELL_MEASUREMENT_REFLN
data items.
cell_measurement.temp
The temperature in kelvins at which the unit-cell parameters
were measured (not the temperature of synthesis).
cell_measurement.temp_esd
The standard uncertainty (estimated standard deviation)
of attribute temp in category cell_measurement.
cell_measurement.theta_max
The maximum theta angle of reflections used to measure
the unit cell in degrees.
cell_measurement.theta_min
The minimum theta angle of reflections used to measure
the unit cell in degrees.
cell_measurement.wavelength
The wavelength in angstroms of the radiation used to measure
the unit cell. If this is not specified, the wavelength is
assumed to be that specified in the category
DIFFRN_RADIATION_WAVELENGTH.
cell_measurement.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
cell_measurement_refln
Data items in the CELL_MEASUREMENT_REFLN category record
details about the reflections used to determine the
crystallographic cell parameters.
The CELL_MEASUREMENT_REFLN data items would in general be used
only for diffractometer data.
Example 1 - extracted from the CAD-4 listing of Rb~2~S~2~O~6~ at room
temperature (unpublished).
<PDBx:cell_measurement_reflnCategory>
<PDBx:cell_measurement_refln index_h="-2" index_k="4" index_l="1">
<PDBx:theta>8.67</PDBx:theta>
</PDBx:cell_measurement_refln>
<PDBx:cell_measurement_refln index_h="0" index_k="3" index_l="2">
<PDBx:theta>9.45</PDBx:theta>
</PDBx:cell_measurement_refln>
<PDBx:cell_measurement_refln index_h="3" index_k="0" index_l="2">
<PDBx:theta>9.46</PDBx:theta>
</PDBx:cell_measurement_refln>
<PDBx:cell_measurement_refln index_h="-3" index_k="4" index_l="1">
<PDBx:theta>8.93</PDBx:theta>
</PDBx:cell_measurement_refln>
<PDBx:cell_measurement_refln index_h="-2" index_k="1" index_l="-2">
<PDBx:theta>7.53</PDBx:theta>
</PDBx:cell_measurement_refln>
<PDBx:cell_measurement_refln index_h="10" index_k="0" index_l="0">
<PDBx:theta>23.77</PDBx:theta>
</PDBx:cell_measurement_refln>
<PDBx:cell_measurement_refln index_h="0" index_k="10" index_l="0">
<PDBx:theta>23.78</PDBx:theta>
</PDBx:cell_measurement_refln>
<PDBx:cell_measurement_refln index_h="-5" index_k="4" index_l="1">
<PDBx:theta>11.14</PDBx:theta>
</PDBx:cell_measurement_refln>
</PDBx:cell_measurement_reflnCategory>
0
1
1
1
1
cell_measurement_reflnCategory
This property indicates that datablock
has a category element cell_measurement_refln.
cell_measurement_reflnItem
Abstract Datatype property for cell_measurement_refln items.
reference_to_cell_measurement_refln
cross-reference to cell_measurement_refln
cell_measurement_refln.theta
Theta angle for a reflection used for measurement of
the unit cell in degrees.
cell_measurement_refln.index_h
Miller index h of a reflection used for measurement of the unit
cell.
cell_measurement_refln.index_k
Miller index k of a reflection used for measurement of the unit
cell.
cell_measurement_refln.index_l
Miller index l of a reflection used for measurement of the unit
cell.
chem_comp
Data items in the CHEM_COMP category give details about each
of the chemical components from which the relevant chemical
structures can be constructed, such as name, mass or charge.
The related categories CHEM_COMP_ATOM, CHEM_COMP_BOND,
CHEM_COMP_ANGLE etc. describe the detailed geometry of these
chemical components.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:chem_compCategory>
<PDBx:chem_comp id="phe">
<PDBx:model_source>1987 Protin/Prolsq Ideals file</PDBx:model_source>
<PDBx:name>phenylalanine</PDBx:name>
</PDBx:chem_comp>
<PDBx:chem_comp id="val">
<PDBx:model_source>1987 Protin/Prolsq Ideals file</PDBx:model_source>
<PDBx:name>alanine</PDBx:name>
</PDBx:chem_comp>
</PDBx:chem_compCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
chem_compCategory
This property indicates that datablock
has a category element chem_comp.
chem_compItem
Abstract Datatype property for chem_comp items.
reference_to_chem_comp
cross-reference to chem_comp
chem_comp.formula
The formula for the chemical component. Formulae are written
according to the following rules:
(1) Only recognized element symbols may be used.
(2) Each element symbol is followed by a 'count' number. A count
of '1' may be omitted.
(3) A space or parenthesis must separate each cluster of
(element symbol + count), but in general parentheses are
not used.
(4) The order of elements depends on whether carbon is
present or not. If carbon is present, the order should be:
C, then H, then the other elements in alphabetical order
of their symbol. If carbon is not present, the elements
are listed purely in alphabetic order of their symbol. This
is the 'Hill' system used by Chemical Abstracts.
C18 H19 N7 O8 S
chem_comp.formula_weight
Formula mass in daltons of the chemical component.
chem_comp.model_details
A description of special aspects of the generation of the
coordinates for the model of the component.
geometry idealized but not minimized
chem_comp.model_erf
A pointer to an external reference file from which the atomic
description of the component is taken.
chem_comp.model_source
The source of the coordinates for the model of the component.
CSD entry ABCDEF
built using Quanta/Charmm
chem_comp.mon_nstd_class
A description of the class of a nonstandard monomer if the
nonstandard monomer represents a modification of a
standard monomer.
iodinated base
phosphorylated amino acid
brominated base
modified amino acid
glycosylated amino acid
chem_comp.mon_nstd_details
A description of special details of a nonstandard monomer.
no
n
yes
y
'yes' indicates that this is a 'standard' monomer, 'no'
indicates that it is 'nonstandard'. Nonstandard monomers
should be described in more detail using the
_chem_comp.mon_nstd_parent, _chem_comp.mon_nstd_class and
attribute mon_nstd_details in category chem_comp data items.
chem_comp.mon_nstd_parent
The name of the parent monomer of the nonstandard monomer,
if the nonstandard monomer represents a modification of a
standard monomer.
tyrosine
cytosine
chem_comp.mon_nstd_parent_comp_id
The identifier for the parent component of the nonstandard
component. May be be a comma separated list if this component
is derived from multiple components.
Items in this indirectly point to attribute id in category chem_comp in
the CHEM_COMP category.
chem_comp.name
The full name of the component.
alanine
valine
adenine
cytosine
chem_comp.number_atoms_all
The total number of atoms in the component.
chem_comp.number_atoms_nh
The number of non-hydrogen atoms in the component.
chem_comp.one_letter_code
For standard polymer components, the one-letter code for
the component. For non-standard polymer components, the
one-letter code for parent component if this exists;
otherwise, the one-letter code should be given as 'X'.
alanine or adenine
A
ambiguous asparagine/aspartic acid
B
arginine
R
asparagine
N
aspartic acid
D
cysteine or cystine or cytosine
C
glutamine
Q
glutamic acid
E
ambiguous glutamine/glutamic acid
Z
glycine or guanine
G
histidine
H
isoleucine
I
leucine
L
lysine
K
methionine
M
phenylalanine
F
proline
P
serine
S
threonine or thymine
T
tryptophan
W
tyrosine
Y
valine
V
uracil
U
water
O
other
X
chem_comp.pdbx_ambiguous_flag
A preliminary classification used by PDB to indicate
that the chemistry of this component while described
as clearly as possible is still ambiguous. Software
tools may not be able to process this component
definition.
chem_comp.pdbx_component_no
A serial number used by PDB in the FORMUL record.
3
chem_comp.pdbx_formal_charge
The net integer charge assigned to this component. This is the
formal charge assignment normally found in chemical diagrams.
chem_comp.pdbx_ideal_coordinates_details
This data item identifies the source of the ideal coordinates in the
component definition.
Y
N
This data item identifies if ideal coordinates are missing in this definition.
chem_comp.pdbx_initial_date
Date component was added to database.
chem_comp.pdbx_model_coordinates_db_code
This data item identifies the PDB database code from which the heavy
atom model coordinates were obtained.
chem_comp.pdbx_model_coordinates_details
This data item provides additional details about the model coordinates
in the component definition.
Y
N
This data item identifies if model coordinates are missing in this definition.
chem_comp.pdbx_modification_details
For nonstandard components a text description
of modification of the parent component.
ATP
chem_comp.pdbx_modified_date
Date component was last modified.
MSD
PDBJ
RCSB
This data item identifies the deposition site that processed
this chemical component defintion.
REL
HOLD
HPUB
OBS
DEL
This data item holds the current release status for the component.
chem_comp.pdbx_replaced_by
Identifies the attribute id in category chem_comp of the component that
has replaced this component.
q11
tvx
chem_comp.pdbx_replaces
Identifies the attribute id's in category chem_comp of the components
which have been replaced by this component.
Multiple id codes should be separated by commas.
q11
tvx,atv
chem_comp.pdbx_subcomponent_list
The list of subcomponents contained in this component.
TSM DPH HIS CHF EMR
chem_comp.pdbx_synonyms
Synonym list for the component.
ATP
chem_comp.pdbx_type
A preliminary classification used by PDB.
chem_comp.three_letter_code
For standard polymer components, the common three-letter code for
the component. Non-standard polymer components and non-polymer
components are also assigned three-letter-codes.
For ambiguous polymer components three-letter code should
be given as 'UNK'. Ambiguous ions are assigned the code 'UNX'.
Ambiguous non-polymer components are assigned the code 'UNL'.
alanine
ALA
arginine
ARG
asparagine
ASN
aspartic acid
ASP
ambiguous asparagine/aspartic acid
ASX
cysteine
CYS
glutamine
GLN
glutamic acid
GLU
glycine
GLY
ambiguous glutamine/glutamic acid
GLX
histidine
HIS
isoleucine
ILE
leucine
LEU
lysine
LYS
methionine
MET
phenylalanine
PHE
proline
PRO
serine
SER
threonine
THR
tryptophan
TRP
tyrosine
TRY
valine
VAL
1-methyladenosine
1MA
5-methylcytosine
5MC
2(prime)-O-methylcytodine
OMC
1-methylguanosine
1MG
N(2)-methylguanosine
2MG
N(2)-dimethylguanosine
M2G
7-methylguanosine
7MG
2(prime)-O-methylguanosine
0MG
dihydrouridine
H2U
ribosylthymidine
5MU
pseudouridine
PSU
acetic acid
ACE
formic acid
FOR
water
HOH
other
UNK
D-peptide linking
L-peptide linking
D-peptide NH3 amino terminus
L-peptide NH3 amino terminus
D-peptide COOH carboxy terminus
L-peptide COOH carboxy terminus
DNA linking
RNA linking
L-RNA linking
L-DNA linking
DNA OH 5 prime terminus
RNA OH 5 prime terminus
DNA OH 3 prime terminus
RNA OH 3 prime terminus
D-saccharide 1,4 and 1,4 linking
L-saccharide 1,4 and 1,4 linking
D-saccharide 1,4 and 1,6 linking
L-saccharide 1,4 and 1,6 linking
L-saccharide
D-saccharide
saccharide
non-polymer
peptide linking
peptide-like
other
For standard polymer components, the type of the monomer.
Note that monomers that will form polymers are of three types:
linking monomers, monomers with some type of N-terminal (or 5')
cap and monomers with some type of C-terminal (or 3') cap.
chem_comp.id
The value of attribute id in category chem_comp must uniquely identify each item in
the CHEM_COMP list.
For protein polymer entities, this is the three-letter code for
the amino acid.
For nucleic acid polymer entities, this is the one-letter code
for the base.
ALA
VAL
DG
C
chem_comp_angle
Data items in the CHEM_COMP_ANGLE category record details about
angles in a chemical component. Angles are designated by three
atoms, with the second atom forming the vertex of the angle.
Target values may be specified as angles in degrees, as a
distance between the first and third atoms, or both.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:chem_comp_angleCategory>
<PDBx:chem_comp_angle atom_id_1="N" atom_id_2="CA" atom_id_3="C" comp_id="PHE">
<PDBx:value_angle>110.8</PDBx:value_angle>
</PDBx:chem_comp_angle>
<PDBx:chem_comp_angle atom_id_1="N" atom_id_2="CA" atom_id_3="CB" comp_id="PHE">
<PDBx:value_angle>110.1</PDBx:value_angle>
</PDBx:chem_comp_angle>
<PDBx:chem_comp_angle atom_id_1="C" atom_id_2="CA" atom_id_3="CB" comp_id="PHE">
<PDBx:value_angle>110.3</PDBx:value_angle>
</PDBx:chem_comp_angle>
<PDBx:chem_comp_angle atom_id_1="C" atom_id_2="CA" atom_id_3="HA" comp_id="PHE">
<PDBx:value_angle>108.3</PDBx:value_angle>
</PDBx:chem_comp_angle>
<PDBx:chem_comp_angle atom_id_1="CA" atom_id_2="C" atom_id_3="O" comp_id="PHE">
<PDBx:value_angle>118.4</PDBx:value_angle>
</PDBx:chem_comp_angle>
<PDBx:chem_comp_angle atom_id_1="CA" atom_id_2="C" atom_id_3="OXT" comp_id="PHE">
<PDBx:value_angle>117.8</PDBx:value_angle>
</PDBx:chem_comp_angle>
<PDBx:chem_comp_angle atom_id_1="CA" atom_id_2="CB" atom_id_3="CG" comp_id="PHE">
<PDBx:value_angle>114.0</PDBx:value_angle>
</PDBx:chem_comp_angle>
<PDBx:chem_comp_angle atom_id_1="O" atom_id_2="C" atom_id_3="OXT" comp_id="PHE">
<PDBx:value_angle>123.8</PDBx:value_angle>
</PDBx:chem_comp_angle>
<PDBx:chem_comp_angle atom_id_1="CB" atom_id_2="CG" atom_id_3="CD1" comp_id="PHE">
<PDBx:value_angle>120.8</PDBx:value_angle>
</PDBx:chem_comp_angle>
<PDBx:chem_comp_angle atom_id_1="CB" atom_id_2="CG" atom_id_3="CD2" comp_id="PHE">
<PDBx:value_angle>120.5</PDBx:value_angle>
</PDBx:chem_comp_angle>
</PDBx:chem_comp_angleCategory>
0
1
0
1
0
1
0
1
1
1
1
1
chem_comp_angleCategory
This property indicates that datablock
has a category element chem_comp_angle.
chem_comp_angleItem
Abstract Datatype property for chem_comp_angle items.
reference_to_chem_comp_angle
cross-reference to chem_comp_angle
chem_comp_angle.value_angle
The value that should be taken as the target value for the angle
associated with the specified atoms, expressed in degrees.
chem_comp_angle.value_angle_esd
The standard uncertainty (estimated standard deviation)
of attribute value_angle in category chem_comp_angle.
chem_comp_angle.value_dist
The value that should be taken as the target value for the angle
associated with the specified atoms, expressed as the distance
between the atoms specified by attribute atom_id_1 in category chem_comp_angle and
attribute atom_id_3 in category chem_comp_angle.
chem_comp_angle.value_dist_esd
The standard uncertainty (estimated standard deviation)
of attribute value_dist in category chem_comp_angle.
chem_comp_angle.atom_id_1
The ID of the first of the three atoms that define the angle.
This data item is a pointer to attribute atom_id in category chem_comp_atom in the
CHEM_COMP_ATOM category.
chem_comp_angle.atom_id_2
The ID of the second of the three atoms that define the angle.
The second atom is taken to be the apex of the angle.
This data item is a pointer to attribute atom_id in category chem_comp_atom in the
CHEM_COMP_ATOM category.
chem_comp_angle.atom_id_3
The ID of the third of the three atoms that define the angle.
This data item is a pointer to attribute atom_id in category chem_comp_atom in the
CHEM_COMP_ATOM category.
chem_comp_angle.comp_id
This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP
category.
chem_comp_atom
Data items in the CHEM_COMP_ATOM category record details about
the atoms in a chemical component. Specifying the atomic
coordinates for the components in this category is an
alternative to specifying the structure of the component
via bonds, angles, planes etc. in the appropriate
CHEM_COMP subcategories.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:chem_comp_atomCategory>
<PDBx:chem_comp_atom atom_id="N" comp_id="phe">
<PDBx:model_Cartn_x>1.20134</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>0.84658</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z>
<PDBx:substruct_code>main</PDBx:substruct_code>
<PDBx:type_symbol>N</PDBx:type_symbol>
</PDBx:chem_comp_atom>
<PDBx:chem_comp_atom atom_id="CA" comp_id="phe">
<PDBx:model_Cartn_x>0.00000</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>0.00000</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z>
<PDBx:substruct_code>main</PDBx:substruct_code>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chem_comp_atom>
<PDBx:chem_comp_atom atom_id="C" comp_id="phe">
<PDBx:model_Cartn_x>-1.25029</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>0.88107</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z>
<PDBx:substruct_code>main</PDBx:substruct_code>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chem_comp_atom>
<PDBx:chem_comp_atom atom_id="O" comp_id="phe">
<PDBx:model_Cartn_x>-2.18525</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>0.66029</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>-0.78409</PDBx:model_Cartn_z>
<PDBx:substruct_code>main</PDBx:substruct_code>
<PDBx:type_symbol>O</PDBx:type_symbol>
</PDBx:chem_comp_atom>
<PDBx:chem_comp_atom atom_id="CB" comp_id="phe">
<PDBx:model_Cartn_x>0.00662</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>-1.03603</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>1.11081</PDBx:model_Cartn_z>
<PDBx:substruct_code>side</PDBx:substruct_code>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chem_comp_atom>
<PDBx:chem_comp_atom atom_id="CG" comp_id="phe">
<PDBx:model_Cartn_x>0.03254</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>-0.49711</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>2.50951</PDBx:model_Cartn_z>
<PDBx:substruct_code>side</PDBx:substruct_code>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chem_comp_atom>
<PDBx:chem_comp_atom atom_id="CD1" comp_id="phe">
<PDBx:model_Cartn_x>-1.15813</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>-0.12084</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>3.13467</PDBx:model_Cartn_z>
<PDBx:substruct_code>side</PDBx:substruct_code>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chem_comp_atom>
<PDBx:chem_comp_atom atom_id="CE1" comp_id="phe">
<PDBx:model_Cartn_x>-1.15720</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>0.38038</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>4.42732</PDBx:model_Cartn_z>
<PDBx:substruct_code>side</PDBx:substruct_code>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chem_comp_atom>
<PDBx:chem_comp_atom atom_id="CZ" comp_id="phe">
<PDBx:model_Cartn_x>0.05385</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>0.51332</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>5.11032</PDBx:model_Cartn_z>
<PDBx:substruct_code>side</PDBx:substruct_code>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chem_comp_atom>
<PDBx:chem_comp_atom atom_id="CE2" comp_id="phe">
<PDBx:model_Cartn_x>1.26137</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>0.11613</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>4.50975</PDBx:model_Cartn_z>
<PDBx:substruct_code>side</PDBx:substruct_code>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chem_comp_atom>
<PDBx:chem_comp_atom atom_id="CD2" comp_id="phe">
<PDBx:model_Cartn_x>1.23668</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>-0.38351</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>3.20288</PDBx:model_Cartn_z>
<PDBx:substruct_code>side</PDBx:substruct_code>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chem_comp_atom>
<PDBx:chem_comp_atom atom_id="N" comp_id="val">
<PDBx:model_Cartn_x>1.20134</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>0.84658</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z>
<PDBx:substruct_code>main</PDBx:substruct_code>
<PDBx:type_symbol>N</PDBx:type_symbol>
</PDBx:chem_comp_atom>
<PDBx:chem_comp_atom atom_id="CA" comp_id="val">
<PDBx:model_Cartn_x>0.00000</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>0.00000</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z>
<PDBx:substruct_code>main</PDBx:substruct_code>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chem_comp_atom>
<PDBx:chem_comp_atom atom_id="C" comp_id="val">
<PDBx:model_Cartn_x>-1.25029</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>0.88107</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z>
<PDBx:substruct_code>main</PDBx:substruct_code>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chem_comp_atom>
<PDBx:chem_comp_atom atom_id="O" comp_id="val">
<PDBx:model_Cartn_x>-2.18525</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>0.66029</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>-0.78409</PDBx:model_Cartn_z>
<PDBx:substruct_code>main</PDBx:substruct_code>
<PDBx:type_symbol>O</PDBx:type_symbol>
</PDBx:chem_comp_atom>
<PDBx:chem_comp_atom atom_id="CB" comp_id="val">
<PDBx:model_Cartn_x>0.05260</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>-0.99339</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>1.17429</PDBx:model_Cartn_z>
<PDBx:substruct_code>side</PDBx:substruct_code>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chem_comp_atom>
<PDBx:chem_comp_atom atom_id="CG1" comp_id="val">
<PDBx:model_Cartn_x>-0.13288</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>-0.31545</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>2.52668</PDBx:model_Cartn_z>
<PDBx:substruct_code>side</PDBx:substruct_code>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chem_comp_atom>
<PDBx:chem_comp_atom atom_id="CG2" comp_id="val">
<PDBx:model_Cartn_x>-0.94265</PDBx:model_Cartn_x>
<PDBx:model_Cartn_y>-2.12930</PDBx:model_Cartn_y>
<PDBx:model_Cartn_z>0.99811</PDBx:model_Cartn_z>
<PDBx:substruct_code>side</PDBx:substruct_code>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chem_comp_atom>
</PDBx:chem_comp_atomCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
chem_comp_atomCategory
This property indicates that datablock
has a category element chem_comp_atom.
chem_comp_atomItem
Abstract Datatype property for chem_comp_atom items.
reference_to_chem_comp_atom
cross-reference to chem_comp_atom
chem_comp_atom.alt_atom_id
An alternative identifier for the atom. This data item would be
used in cases where alternative nomenclatures exist for labelling
atoms in a group.
chem_comp_atom.charge
The net integer charge assigned to this atom. This is the
formal charge assignment normally found in chemical diagrams.
for an ammonium nitrogen
1
for a chloride ion
-1
chem_comp_atom.model_Cartn_x
The x component of the coordinates for this atom in this
component specified as orthogonal angstroms. The choice of
reference axis frame for the coordinates is arbitrary.
The set of coordinates input for the entity here is intended to
correspond to the atomic model used to generate restraints for
structure refinement, not to atom sites in the ATOM_SITE
list.
chem_comp_atom.model_Cartn_x_esd
The standard uncertainty (estimated standard deviation)
of attribute model_Cartn_x in category chem_comp_atom.
chem_comp_atom.model_Cartn_y
The y component of the coordinates for this atom in this
component specified as orthogonal angstroms. The choice of
reference axis frame for the coordinates is arbitrary.
The set of coordinates input for the entity here is intended to
correspond to the atomic model used to generate restraints for
structure refinement, not to atom sites in the ATOM_SITE
list.
chem_comp_atom.model_Cartn_y_esd
The standard uncertainty (estimated standard deviation)
of attribute model_Cartn_y in category chem_comp_atom.
chem_comp_atom.model_Cartn_z
The z component of the coordinates for this atom in this
component specified as orthogonal angstroms. The choice of
reference axis frame for the coordinates is arbitrary.
The set of coordinates input for the entity here is intended to
correspond to the atomic model used to generate restraints for
structure refinement, not to atom sites in the ATOM_SITE
list.
chem_comp_atom.model_Cartn_z_esd
The standard uncertainty (estimated standard deviation)
of attribute model_Cartn_z in category chem_comp_atom.
chem_comp_atom.partial_charge
The partial charge assigned to this atom.
chem_comp_atom.pdbx_align
Atom name alignment offset in PDB atom field.
chem_comp_atom.pdbx_alt_atom_id
An alternative identifier for the atom. This data item would be
used in cases where alternative nomenclatures exist for labelling
atoms in a group.
chem_comp_atom.pdbx_alt_comp_id
An alternative identifier for the atom. This data item would be
used in cases where alternative nomenclatures exist for labelling
atoms in a group.
Y
N
A flag indicating an aromatic atom.
chem_comp_atom.pdbx_component_atom_id
The atom identifier in the subcomponent where a
larger component has been divided subcomponents.
CB
CA
CG
chem_comp_atom.pdbx_component_comp_id
The component identifier for the subcomponent where a
larger component has been divided subcomponents.
HIS
PRO
Y
N
A flag indicating a leaving atom.
chem_comp_atom.pdbx_model_Cartn_x_ideal
An alternative x component of the coordinates for this atom in this
component specified as orthogonal angstroms.
chem_comp_atom.pdbx_model_Cartn_y_ideal
An alternative y component of the coordinates for this atom in this
component specified as orthogonal angstroms.
chem_comp_atom.pdbx_model_Cartn_z_ideal
An alternative z component of the coordinates for this atom in this
component specified as orthogonal angstroms.
chem_comp_atom.pdbx_ordinal
Ordinal index for the component atom list.
R
S
N
The chiral configuration of the atom that is a chiral center.
main
side
base
phos
sugar
none
This data item assigns the atom to a substructure of the
component, if appropriate.
chem_comp_atom.type_symbol
The code used to identify the atom species representing
this atom type. Normally this code is the element
symbol.
C
N
O
chem_comp_atom.atom_id
The value of attribute atom_id in category chem_comp_atom must uniquely identify
each atom in each monomer in the CHEM_COMP_ATOM list.
The atom identifiers need not be unique over all atoms in the
data block; they need only be unique for each atom in a
component.
Note that this item need not be a number; it can be any unique
identifier.
chem_comp_atom.comp_id
This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP
category.
chem_comp_bond
Data items in the CHEM_COMP_BOND category record details about
the bonds between atoms in a chemical component. Target values
may be specified as bond orders, as a distance between the two
atoms, or both.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:chem_comp_bondCategory>
<PDBx:chem_comp_bond atom_id_1="N" atom_id_2="CA" comp_id="phe">
<PDBx:value_order>sing</PDBx:value_order>
</PDBx:chem_comp_bond>
<PDBx:chem_comp_bond atom_id_1="CA" atom_id_2="C" comp_id="phe">
<PDBx:value_order>sing</PDBx:value_order>
</PDBx:chem_comp_bond>
<PDBx:chem_comp_bond atom_id_1="C" atom_id_2="O" comp_id="phe">
<PDBx:value_order>doub</PDBx:value_order>
</PDBx:chem_comp_bond>
<PDBx:chem_comp_bond atom_id_1="CB" atom_id_2="CA" comp_id="phe">
<PDBx:value_order>sing</PDBx:value_order>
</PDBx:chem_comp_bond>
<PDBx:chem_comp_bond atom_id_1="CB" atom_id_2="CG" comp_id="phe">
<PDBx:value_order>sing</PDBx:value_order>
</PDBx:chem_comp_bond>
<PDBx:chem_comp_bond atom_id_1="CG" atom_id_2="CD1" comp_id="phe">
<PDBx:value_order>arom</PDBx:value_order>
</PDBx:chem_comp_bond>
<PDBx:chem_comp_bond atom_id_1="CD1" atom_id_2="CE1" comp_id="phe">
<PDBx:value_order>arom</PDBx:value_order>
</PDBx:chem_comp_bond>
<PDBx:chem_comp_bond atom_id_1="CE1" atom_id_2="CZ" comp_id="phe">
<PDBx:value_order>arom</PDBx:value_order>
</PDBx:chem_comp_bond>
<PDBx:chem_comp_bond atom_id_1="CZ" atom_id_2="CE2" comp_id="phe">
<PDBx:value_order>arom</PDBx:value_order>
</PDBx:chem_comp_bond>
<PDBx:chem_comp_bond atom_id_1="CE2" atom_id_2="CD2" comp_id="phe">
<PDBx:value_order>arom</PDBx:value_order>
</PDBx:chem_comp_bond>
<PDBx:chem_comp_bond atom_id_1="CD2" atom_id_2="CG" comp_id="phe">
<PDBx:value_order>arom</PDBx:value_order>
</PDBx:chem_comp_bond>
<PDBx:chem_comp_bond atom_id_1="N" atom_id_2="CA" comp_id="val">
<PDBx:value_order>sing</PDBx:value_order>
</PDBx:chem_comp_bond>
<PDBx:chem_comp_bond atom_id_1="CA" atom_id_2="C" comp_id="val">
<PDBx:value_order>sing</PDBx:value_order>
</PDBx:chem_comp_bond>
<PDBx:chem_comp_bond atom_id_1="C" atom_id_2="O" comp_id="val">
<PDBx:value_order>doub</PDBx:value_order>
</PDBx:chem_comp_bond>
<PDBx:chem_comp_bond atom_id_1="CB" atom_id_2="CA" comp_id="val">
<PDBx:value_order>sing</PDBx:value_order>
</PDBx:chem_comp_bond>
<PDBx:chem_comp_bond atom_id_1="CB" atom_id_2="CG1" comp_id="val">
<PDBx:value_order>sing</PDBx:value_order>
</PDBx:chem_comp_bond>
<PDBx:chem_comp_bond atom_id_1="CB" atom_id_2="CG2" comp_id="val">
<PDBx:value_order>sing</PDBx:value_order>
</PDBx:chem_comp_bond>
</PDBx:chem_comp_bondCategory>
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
chem_comp_bondCategory
This property indicates that datablock
has a category element chem_comp_bond.
chem_comp_bondItem
Abstract Datatype property for chem_comp_bond items.
reference_to_chem_comp_bond
cross-reference to chem_comp_bond
Y
N
A flag indicating an aromatic bond.
chem_comp_bond.pdbx_ordinal
Ordinal index for the component bond list.
E
Z
N
Stereochemical configuration across a double bond.
chem_comp_bond.value_dist
The value that should be taken as the target for the chemical
bond associated with the specified atoms, expressed as a
distance.
chem_comp_bond.value_dist_esd
The standard uncertainty (estimated standard deviation)
of attribute value_dist in category chem_comp_bond.
sing
doub
trip
quad
arom
poly
delo
pi
The value that should be taken as the target for the chemical
bond associated with the specified atoms, expressed as a bond
order.
chem_comp_bond.atom_id_1
The ID of the first of the two atoms that define the bond.
This data item is a pointer to attribute atom_id in category chem_comp_atom in the
CHEM_COMP_ATOM category.
chem_comp_bond.atom_id_2
The ID of the second of the two atoms that define the bond.
This data item is a pointer to attribute atom_id in category chem_comp_atom in the
CHEM_COMP_ATOM category.
chem_comp_bond.comp_id
This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP
category.
chem_comp_chir
Data items in the CHEM_COMP_CHIR category provide details about
the chiral centres in a chemical component. The atoms bonded
to the chiral atom are specified in the CHEM_COMP_CHIR_ATOM
category.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:chem_comp_chirCategory>
<PDBx:chem_comp_chir comp_id="phe" id="phe1">
<PDBx:atom_id>CA</PDBx:atom_id>
</PDBx:chem_comp_chir>
<PDBx:chem_comp_chir comp_id="val" id="val1">
<PDBx:atom_id>CA</PDBx:atom_id>
</PDBx:chem_comp_chir>
</PDBx:chem_comp_chirCategory>
0
1
1
1
0
1
0
1
0
1
0
1
0
1
1
1
chem_comp_chirCategory
This property indicates that datablock
has a category element chem_comp_chir.
chem_comp_chirItem
Abstract Datatype property for chem_comp_chir items.
reference_to_chem_comp_chir
cross-reference to chem_comp_chir
R
S
The chiral configuration of the atom that is a chiral centre.
chem_comp_chir.atom_id
The ID of the atom that is a chiral centre.
This data item is a pointer to attribute atom_id in category chem_comp_atom in the
CHEM_COMP_ATOM category.
chem_comp_chir.number_atoms_all
The total number of atoms bonded to the atom specified by
attribute atom_id in category chem_comp_chir.
chem_comp_chir.number_atoms_nh
The number of non-hydrogen atoms bonded to the atom specified by
attribute atom_id in category chem_comp_chir.
sign
nosign
A flag to indicate whether a chiral volume should match the
standard value in both magnitude and sign, or in magnitude only.
chem_comp_chir.volume_three
The chiral volume, V~c~, for chiral centres that involve a chiral
atom bonded to three non-hydrogen atoms and one hydrogen atom.
V~c~ = V1 * (V2 X V3)
V1 = the vector distance from the atom specified by
attribute atom_id in category chem_comp_chir to the first atom in the
CHEM_COMP_CHIR_ATOM list
V2 = the vector distance from the atom specified by
attribute atom_id in category chem_comp_chir to the second atom in the
CHEM_COMP_CHIR_ATOM list
V3 = the vector distance from the atom specified by
attribute atom_id in category chem_comp_chir to the third atom in the
CHEM_COMP_CHIR_ATOM list
* = the vector dot product
X = the vector cross product
chem_comp_chir.volume_three_esd
The standard uncertainty (estimated standard deviation)
of attribute volume_three in category chem_comp_chir.
chem_comp_chir.comp_id
This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP
category.
chem_comp_chir.id
The value of attribute id in category chem_comp_chir must uniquely identify a record
in the CHEM_COMP_CHIR list.
chem_comp_chir_atom
Data items in the CHEM_COMP_CHIR_ATOM category enumerate the
atoms bonded to a chiral atom within a chemical component.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:chem_comp_chir_atomCategory>
<PDBx:chem_comp_chir_atom atom_id="N" chir_id="1" comp_id="phe"></PDBx:chem_comp_chir_atom>
<PDBx:chem_comp_chir_atom atom_id="C" chir_id="1" comp_id="phe"></PDBx:chem_comp_chir_atom>
<PDBx:chem_comp_chir_atom atom_id="CB" chir_id="1" comp_id="phe"></PDBx:chem_comp_chir_atom>
<PDBx:chem_comp_chir_atom atom_id="N" chir_id="1" comp_id="val"></PDBx:chem_comp_chir_atom>
<PDBx:chem_comp_chir_atom atom_id="C" chir_id="1" comp_id="val"></PDBx:chem_comp_chir_atom>
<PDBx:chem_comp_chir_atom atom_id="CB" chir_id="1" comp_id="val"></PDBx:chem_comp_chir_atom>
</PDBx:chem_comp_chir_atomCategory>
0
1
1
1
1
chem_comp_chir_atomCategory
This property indicates that datablock
has a category element chem_comp_chir_atom.
chem_comp_chir_atomItem
Abstract Datatype property for chem_comp_chir_atom items.
reference_to_chem_comp_chir_atom
cross-reference to chem_comp_chir_atom
chem_comp_chir_atom.dev
The standard uncertainty (estimated standard deviation)
of the position of this atom from the plane defined by
all of the atoms in the plane.
chem_comp_chir_atom.atom_id
The ID of an atom bonded to the chiral atom.
This data item is a pointer to attribute atom_id in category chem_comp_atom in the
CHEM_COMP_ATOM category.
chem_comp_chir_atom.chir_id
This data item is a pointer to attribute id in category chem_comp_chir in the
CHEM_COMP_CHIR category.
chem_comp_chir_atom.comp_id
This data item is a pointer to attribute id in category chem_comp in the
CHEM_COMP category.
chem_comp_link
Data items in the CHEM_COMP_LINK category give details about
the links between chemical components.
0
1
1
1
1
1
1
chem_comp_linkCategory
This property indicates that datablock
has a category element chem_comp_link.
chem_comp_linkItem
Abstract Datatype property for chem_comp_link items.
reference_to_chem_comp_link
cross-reference to chem_comp_link
chem_comp_link.details
A description of special aspects of a link between
chemical components in the structure.
chem_comp_link.type_comp_1
The type of the first of the two components joined by the
link.
This data item is a pointer to attribute type in category chem_comp in the CHEM_COMP
category.
chem_comp_link.type_comp_2
The type of the second of the two components joined by the
link.
This data item is a pointer to attribute type in category chem_comp in the CHEM_COMP
category.
chem_comp_link.link_id
This data item is a pointer to attribute id in category chem_link in the
CHEM_LINK category.
chem_comp_plane
Data items in the CHEM_COMP_PLANE category provide identifiers
for the planes in a chemical component. The atoms in the plane
are specified in the CHEM_COMP_PLANE_ATOM category.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:chem_comp_planeCategory>
<PDBx:chem_comp_plane comp_id="phe" id="phe1"></PDBx:chem_comp_plane>
</PDBx:chem_comp_planeCategory>
0
1
0
1
1
1
chem_comp_planeCategory
This property indicates that datablock
has a category element chem_comp_plane.
chem_comp_planeItem
Abstract Datatype property for chem_comp_plane items.
reference_to_chem_comp_plane
cross-reference to chem_comp_plane
chem_comp_plane.number_atoms_all
The total number of atoms in the plane.
chem_comp_plane.number_atoms_nh
The number of non-hydrogen atoms in the plane.
chem_comp_plane.comp_id
This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP
category.
chem_comp_plane.id
The value of attribute id in category chem_comp_plane must uniquely identify a record
in the CHEM_COMP_PLANE list.
chem_comp_plane_atom
Data items in the CHEM_COMP_PLANE_ATOM category enumerate the
atoms in a plane within a chemical component.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:chem_comp_plane_atomCategory>
<PDBx:chem_comp_plane_atom atom_id="CB" comp_id="phe" plane_id="phe1"></PDBx:chem_comp_plane_atom>
<PDBx:chem_comp_plane_atom atom_id="CG" comp_id="phe" plane_id="phe1"></PDBx:chem_comp_plane_atom>
<PDBx:chem_comp_plane_atom atom_id="CD1" comp_id="phe" plane_id="phe1"></PDBx:chem_comp_plane_atom>
<PDBx:chem_comp_plane_atom atom_id="CE1" comp_id="phe" plane_id="phe1"></PDBx:chem_comp_plane_atom>
<PDBx:chem_comp_plane_atom atom_id="CZ" comp_id="phe" plane_id="phe1"></PDBx:chem_comp_plane_atom>
<PDBx:chem_comp_plane_atom atom_id="CE2" comp_id="phe" plane_id="phe1"></PDBx:chem_comp_plane_atom>
<PDBx:chem_comp_plane_atom atom_id="CD2" comp_id="phe" plane_id="phe1"></PDBx:chem_comp_plane_atom>
</PDBx:chem_comp_plane_atomCategory>
0
1
1
1
1
chem_comp_plane_atomCategory
This property indicates that datablock
has a category element chem_comp_plane_atom.
chem_comp_plane_atomItem
Abstract Datatype property for chem_comp_plane_atom items.
reference_to_chem_comp_plane_atom
cross-reference to chem_comp_plane_atom
chem_comp_plane_atom.dist_esd
This data item is the standard deviation of the
out-of-plane distance for this atom.
chem_comp_plane_atom.atom_id
The ID of an atom involved in the plane.
This data item is a pointer to attribute atom_id in category chem_comp_atom in the
CHEM_COMP_ATOM category.
chem_comp_plane_atom.comp_id
This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP
category.
chem_comp_plane_atom.plane_id
This data item is a pointer to attribute id in category chem_comp_plane in the
CHEM_COMP_PLANE category.
chem_comp_tor
Data items in the CHEM_COMP_TOR category record details about
the torsion angles in a chemical component. As torsion angles
can have more than one target value, the target values are
specified in the CHEM_COMP_TOR_VALUE category.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:chem_comp_torCategory>
<PDBx:chem_comp_tor comp_id="phe" id="phe_chi1">
<PDBx:atom_id_1>N</PDBx:atom_id_1>
<PDBx:atom_id_2>CA</PDBx:atom_id_2>
<PDBx:atom_id_3>CB</PDBx:atom_id_3>
<PDBx:atom_id_4>CG</PDBx:atom_id_4>
</PDBx:chem_comp_tor>
<PDBx:chem_comp_tor comp_id="phe" id="phe_chi2">
<PDBx:atom_id_1>CA</PDBx:atom_id_1>
<PDBx:atom_id_2>CB</PDBx:atom_id_2>
<PDBx:atom_id_3>CG</PDBx:atom_id_3>
<PDBx:atom_id_4>CD1</PDBx:atom_id_4>
</PDBx:chem_comp_tor>
<PDBx:chem_comp_tor comp_id="phe" id="phe_ring1">
<PDBx:atom_id_1>CB</PDBx:atom_id_1>
<PDBx:atom_id_2>CG</PDBx:atom_id_2>
<PDBx:atom_id_3>CD1</PDBx:atom_id_3>
<PDBx:atom_id_4>CE1</PDBx:atom_id_4>
</PDBx:chem_comp_tor>
<PDBx:chem_comp_tor comp_id="phe" id="phe_ring2">
<PDBx:atom_id_1>CB</PDBx:atom_id_1>
<PDBx:atom_id_2>CG</PDBx:atom_id_2>
<PDBx:atom_id_3>CD2</PDBx:atom_id_3>
<PDBx:atom_id_4>CE2</PDBx:atom_id_4>
</PDBx:chem_comp_tor>
<PDBx:chem_comp_tor comp_id="phe" id="phe_ring3">
<PDBx:atom_id_1>CG</PDBx:atom_id_1>
<PDBx:atom_id_2>CD1</PDBx:atom_id_2>
<PDBx:atom_id_3>CE1</PDBx:atom_id_3>
<PDBx:atom_id_4>CZ</PDBx:atom_id_4>
</PDBx:chem_comp_tor>
<PDBx:chem_comp_tor comp_id="phe" id="phe_ring4">
<PDBx:atom_id_1>CD1</PDBx:atom_id_1>
<PDBx:atom_id_2>CE1</PDBx:atom_id_2>
<PDBx:atom_id_3>CZ</PDBx:atom_id_3>
<PDBx:atom_id_4>CE2</PDBx:atom_id_4>
</PDBx:chem_comp_tor>
<PDBx:chem_comp_tor comp_id="phe" id="phe_ring5">
<PDBx:atom_id_1>CE1</PDBx:atom_id_1>
<PDBx:atom_id_2>CZ</PDBx:atom_id_2>
<PDBx:atom_id_3>CE2</PDBx:atom_id_3>
<PDBx:atom_id_4>CD2</PDBx:atom_id_4>
</PDBx:chem_comp_tor>
</PDBx:chem_comp_torCategory>
1
1
1
1
1
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1
1
1
1
chem_comp_torCategory
This property indicates that datablock
has a category element chem_comp_tor.
chem_comp_torItem
Abstract Datatype property for chem_comp_tor items.
reference_to_chem_comp_tor
cross-reference to chem_comp_tor
chem_comp_tor.atom_id_1
The ID of the first of the four atoms that define the torsion
angle.
This data item is a pointer to attribute atom_id in category chem_comp_atom in the
CHEM_COMP_ATOM category.
chem_comp_tor.atom_id_2
The ID of the second of the four atoms that define the torsion
angle.
This data item is a pointer to attribute atom_id in category chem_comp_atom in the
CHEM_COMP_ATOM category.
chem_comp_tor.atom_id_3
The ID of the third of the four atoms that define the torsion
angle.
This data item is a pointer to attribute atom_id in category chem_comp_atom in the
CHEM_COMP_ATOM category.
chem_comp_tor.atom_id_4
The ID of the fourth of the four atoms that define the torsion
angle.
This data item is a pointer to attribute atom_id in category chem_comp_atom in the
CHEM_COMP_ATOM category.
chem_comp_tor.comp_id
This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP
category.
chem_comp_tor.id
The value of attribute id in category chem_comp_tor must uniquely identify a
record in the CHEM_COMP_TOR list.
chem_comp_tor_value
Data items in the CHEM_COMP_TOR_VALUE category record details
about the target values for the torsion angles enumerated in the
CHEM_COMP_TOR list. Target values may be specified as angles
in degrees, as a distance between the first and fourth atoms, or
both.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:chem_comp_tor_valueCategory>
<PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_chi1">
<PDBx:angle>-60.0</PDBx:angle>
<PDBx:dist>2.88</PDBx:dist>
</PDBx:chem_comp_tor_value>
<PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_chi1">
<PDBx:angle>180.0</PDBx:angle>
<PDBx:dist>3.72</PDBx:dist>
</PDBx:chem_comp_tor_value>
<PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_chi1">
<PDBx:angle>60.0</PDBx:angle>
<PDBx:dist>2.88</PDBx:dist>
</PDBx:chem_comp_tor_value>
<PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_chi2">
<PDBx:angle>90.0</PDBx:angle>
<PDBx:dist>3.34</PDBx:dist>
</PDBx:chem_comp_tor_value>
<PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_chi2">
<PDBx:angle>-90.0</PDBx:angle>
<PDBx:dist>3.34</PDBx:dist>
</PDBx:chem_comp_tor_value>
<PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_ring1">
<PDBx:angle>180.0</PDBx:angle>
<PDBx:dist>3.75</PDBx:dist>
</PDBx:chem_comp_tor_value>
<PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_ring2">
<PDBx:angle>180.0</PDBx:angle>
<PDBx:dist>3.75</PDBx:dist>
</PDBx:chem_comp_tor_value>
<PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_ring3">
<PDBx:angle>0.0</PDBx:angle>
<PDBx:dist>2.80</PDBx:dist>
</PDBx:chem_comp_tor_value>
<PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_ring4">
<PDBx:angle>0.0</PDBx:angle>
<PDBx:dist>2.80</PDBx:dist>
</PDBx:chem_comp_tor_value>
<PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_ring5">
<PDBx:angle>0.0</PDBx:angle>
<PDBx:dist>2.80</PDBx:dist>
</PDBx:chem_comp_tor_value>
</PDBx:chem_comp_tor_valueCategory>
1
1
1
1
0
1
0
1
1
1
chem_comp_tor_valueCategory
This property indicates that datablock
has a category element chem_comp_tor_value.
chem_comp_tor_valueItem
Abstract Datatype property for chem_comp_tor_value items.
reference_to_chem_comp_tor_value
cross-reference to chem_comp_tor_value
chem_comp_tor_value.angle
A value that should be taken as a potential target value for the
torsion angle associated with the specified atoms, expressed in
degrees.
chem_comp_tor_value.angle_esd
The standard uncertainty (estimated standard deviation)
of attribute angle in category chem_comp_tor_value.
chem_comp_tor_value.dist
A value that should be taken as a potential target value for the
torsion angle associated with the specified atoms, expressed as
the distance between the atoms specified by
_chem_comp_tor.atom_id_1 and _chem_comp_tor.atom_id_4 in the
referenced record in the CHEM_COMP_TOR list. Note that the
torsion angle cannot be fully specified by a distance (for
instance, a torsion angle of -60 degree will yield the same
distance as a 60 degree angle). However, the distance
specification can be useful for refinement in situations
in which the angle is already close to the desired value.
chem_comp_tor_value.dist_esd
The standard uncertainty (estimated standard deviation)
of attribute dist in category chem_comp_tor_value.
chem_comp_tor_value.comp_id
This data item is a pointer to attribute comp_id in category chem_comp_atom in the
CHEM_COMP_ATOM category.
chem_comp_tor_value.tor_id
This data item is a pointer to attribute id in category chem_comp_tor in the
CHEM_COMP_TOR category.
chem_link
Data items in the CHEM_LINK category give details about
the links between chemical components.
0
1
1
chem_linkCategory
This property indicates that datablock
has a category element chem_link.
chem_linkItem
Abstract Datatype property for chem_link items.
reference_to_chem_link
cross-reference to chem_link
chem_link.details
A description of special aspects of a link between
chemical components in the structure.
chem_link.id
The value of attribute id in category chem_link must uniquely identify each
item in the CHEM_LINK list.
peptide
oligosaccharide 1,4
DNA
chem_link_angle
Data items in the CHEM_LINK_ANGLE category record details
about angles in a link between chemical components.
Example 1 - Engh & Huber parameters [Acta Cryst. (1991), A47,
392-400] as interpreted by J. P. Priestle (1995). Consistent
Stereochemical Dictionaries for Refinement and Model
Building. CCP4 Daresbury Study Weekend,
DL-CONF-95-001, ISSN 1358-6254. Warrington: Daresbury
Laboratory.
<PDBx:chem_link_angleCategory>
<PDBx:chem_link_angle atom_id_1="N" atom_id_2="CA" atom_id_3="C" link_id="PEPTIDE">
<PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id>
<PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id>
<PDBx:atom_3_comp_id>1</PDBx:atom_3_comp_id>
<PDBx:value_angle>111.2</PDBx:value_angle>
<PDBx:value_angle_esd>2.8</PDBx:value_angle_esd>
</PDBx:chem_link_angle>
<PDBx:chem_link_angle atom_id_1="CA" atom_id_2="C" atom_id_3="O" link_id="PEPTIDE">
<PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id>
<PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id>
<PDBx:atom_3_comp_id>1</PDBx:atom_3_comp_id>
<PDBx:value_angle>120.8</PDBx:value_angle>
<PDBx:value_angle_esd>1.7</PDBx:value_angle_esd>
</PDBx:chem_link_angle>
<PDBx:chem_link_angle atom_id_1="CA" atom_id_2="C" atom_id_3="N" link_id="PEPTIDE">
<PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id>
<PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id>
<PDBx:atom_3_comp_id>2</PDBx:atom_3_comp_id>
<PDBx:value_angle>116.2</PDBx:value_angle>
<PDBx:value_angle_esd>2.0</PDBx:value_angle_esd>
</PDBx:chem_link_angle>
<PDBx:chem_link_angle atom_id_1="O" atom_id_2="C" atom_id_3="N" link_id="PEPTIDE">
<PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id>
<PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id>
<PDBx:atom_3_comp_id>2</PDBx:atom_3_comp_id>
<PDBx:value_angle>123.0</PDBx:value_angle>
<PDBx:value_angle_esd>1.6</PDBx:value_angle_esd>
</PDBx:chem_link_angle>
<PDBx:chem_link_angle atom_id_1="C" atom_id_2="N" atom_id_3="CA" link_id="PEPTIDE">
<PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id>
<PDBx:atom_2_comp_id>2</PDBx:atom_2_comp_id>
<PDBx:atom_3_comp_id>2</PDBx:atom_3_comp_id>
<PDBx:value_angle>121.7</PDBx:value_angle>
<PDBx:value_angle_esd>1.8</PDBx:value_angle_esd>
</PDBx:chem_link_angle>
</PDBx:chem_link_angleCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
chem_link_angleCategory
This property indicates that datablock
has a category element chem_link_angle.
chem_link_angleItem
Abstract Datatype property for chem_link_angle items.
reference_to_chem_link_angle
cross-reference to chem_link_angle
1
2
This data item indicates whether atom 1 is found in the first
or the second of the two components connected by the link.
1
2
This data item indicates whether atom 2 is found in the first
or the second of the two components connected by the link.
1
2
This data item indicates whether atom 3 is found in the first
or the second of the two components connected by the link.
chem_link_angle.value_angle
The value that should be taken as the target value for the angle
associated with the specified atoms, expressed in degrees.
chem_link_angle.value_angle_esd
The standard uncertainty (estimated standard deviation)
of attribute value_angle in category chem_link_angle.
chem_link_angle.value_dist
The value that should be taken as the target value for the angle
associated with the specified atoms, expressed as the distance
between the atoms specified by attribute atom_id_1 in category chem_comp_angle and
attribute atom_id_3 in category chem_comp_angle.
chem_link_angle.value_dist_esd
The standard uncertainty (estimated standard deviation)
of attribute value_dist in category chem_comp_angle.
chem_link_angle.atom_id_1
The ID of the first of the three atoms that define the angle.
An atom with this ID must exist in the component of the type
specified by attribute type_comp_1 in category chem_comp_link (or
attribute type_comp_2 in category chem_comp_link, where the appropriate data item
is indicated by the value of attribute atom_1_comp_id) in category chem_comp_angle.
chem_link_angle.atom_id_2
The ID of the second of the three atoms that define the angle.
The second atom is taken to be the apex of the angle.
An atom with this ID must exist in the component of the type
specified by attribute type_comp_1 in category chem_comp_link (or
attribute type_comp_2 in category chem_comp_link, where the appropriate data item
is indicated by the value of attribute atom_2_comp_id) in category chem_comp_angle.
chem_link_angle.atom_id_3
The ID of the third of the three atoms that define the angle.
An atom with this ID must exist in the component of the type
specified by attribute type_comp_1 in category chem_comp_link (or
attribute type_comp_2 in category chem_comp_link, where the appropriate data item
is indicated by the value of attribute atom_3_comp_id) in category chem_comp_angle.
chem_link_angle.link_id
This data item is a pointer to attribute id in category chem_link in the CHEM_LINK
category.
chem_link_bond
Data items in the CHEM_LINK_BOND category record details about
bonds in a link between components in the chemical structure.
Example 1 - Engh & Huber parameters [Acta Cryst. (1991), A47,
392-400] as interpreted by J. P. Priestle (1995). Consistent
Stereochemical Dictionaries for Refinement and Model
Building. CCP4 Daresbury Study Weekend,
DL-CONF-95-001, ISSN 1358-6254. Warrington: Daresbury
Laboratory.
<PDBx:chem_link_bondCategory>
<PDBx:chem_link_bond atom_id_1="N" atom_id_2="CA" link_id="PEPTIDE">
<PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id>
<PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id>
<PDBx:value_dist>1.458</PDBx:value_dist>
<PDBx:value_dist_esd>0.019</PDBx:value_dist_esd>
</PDBx:chem_link_bond>
<PDBx:chem_link_bond atom_id_1="CA" atom_id_2="C" link_id="PEPTIDE">
<PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id>
<PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id>
<PDBx:value_dist>1.525</PDBx:value_dist>
<PDBx:value_dist_esd>0.021</PDBx:value_dist_esd>
</PDBx:chem_link_bond>
<PDBx:chem_link_bond atom_id_1="C" atom_id_2="N" link_id="PEPTIDE">
<PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id>
<PDBx:atom_2_comp_id>2</PDBx:atom_2_comp_id>
<PDBx:value_dist>1.329</PDBx:value_dist>
<PDBx:value_dist_esd>0.014</PDBx:value_dist_esd>
</PDBx:chem_link_bond>
<PDBx:chem_link_bond atom_id_1="C" atom_id_2="O" link_id="PEPTIDE">
<PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id>
<PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id>
<PDBx:value_dist>1.231</PDBx:value_dist>
<PDBx:value_dist_esd>0.020</PDBx:value_dist_esd>
</PDBx:chem_link_bond>
</PDBx:chem_link_bondCategory>
0
1
0
1
0
1
0
1
0
1
1
1
1
chem_link_bondCategory
This property indicates that datablock
has a category element chem_link_bond.
chem_link_bondItem
Abstract Datatype property for chem_link_bond items.
reference_to_chem_link_bond
cross-reference to chem_link_bond
1
2
This data item indicates whether atom 1 is found in the first
or the second of the two components connected by the link.
1
2
This data item indicates whether atom 2 is found in the first
or the second of the two chemical components connected by
the link.
chem_link_bond.value_dist
The value that should be taken as the target for the chemical
bond associated with the specified atoms, expressed as a
distance.
chem_link_bond.value_dist_esd
The standard uncertainty (estimated standard deviation)
of attribute value_dist in category chem_link_bond.
sing
doub
trip
quad
arom
poly
delo
pi
The value that should be taken as the target for the chemical
bond associated with the specified atoms, expressed as a bond
order.
chem_link_bond.atom_id_1
The ID of the first of the two atoms that define the bond.
As this data item does not point to a specific atom in a
specific chemical component, it is not a child in the
linkage sense.
chem_link_bond.atom_id_2
The ID of the second of the two atoms that define the bond.
As this data item does not point to a specific atom in a
specific component, it is not a child in the linkage sense.
chem_link_bond.link_id
This data item is a pointer to attribute id in category chem_link in the CHEM_LINK
category.
chem_link_chir
Data items in the CHEM_LINK_CHIR category provide details about
the chiral centres in a link between two chemical components.
The atoms bonded to the chiral atom are specified in the
CHEM_LINK_CHIR_ATOM category.
0
1
0
1
1
1
0
1
0
1
0
1
0
1
0
1
1
1
chem_link_chirCategory
This property indicates that datablock
has a category element chem_link_chir.
chem_link_chirItem
Abstract Datatype property for chem_link_chir items.
reference_to_chem_link_chir
cross-reference to chem_link_chir
1
2
This data item indicates whether the chiral atom is found in the
first or the second of the two components connected by the
link.
R
S
The chiral configuration of the atom that is a chiral centre.
chem_link_chir.atom_id
The ID of the atom that is a chiral centre.
As this data item does not point to a specific atom in a
specific chemical component, it is not a child in the linkage
sense.
chem_link_chir.number_atoms_all
The total number of atoms bonded to the atom specified by
attribute atom_id in category chem_link_chir.
chem_link_chir.number_atoms_nh
The number of non-hydrogen atoms bonded to the atom specified by
attribute atom_id in category chem_link_chir.
sign
nosign
A flag to indicate whether a chiral volume should match the
standard value in both magnitude and sign, or in magnitude only.
chem_link_chir.volume_three
The chiral volume, V(c), for chiral centres that involve a chiral
atom bonded to three non-hydrogen atoms and one hydrogen atom.
V~c~ = V1 * (V2 X V3)
V1 = the vector distance from the atom specified by
attribute atom_id in category chem_link_chir to the first atom in the
CHEM_LINK_CHIR_ATOM list
V2 = the vector distance from the atom specified by
attribute atom_id in category chem_link_chir to the second atom in the
CHEM_LINK_CHIR_ATOM list
V3 = the vector distance from the atom specified by
attribute atom_id in category chem_link_chir to the third atom in the
CHEM_LINK_CHIR_ATOM list
* = the vector dot product
X = the vector cross product
chem_link_chir.volume_three_esd
The standard uncertainty (estimated standard deviation)
of attribute volume_three in category chem_link_chir.
chem_link_chir.id
The value of attribute id in category chem_link_chir must uniquely identify a record
in the CHEM_LINK_CHIR list.
chem_link_chir.link_id
This data item is a pointer to attribute id in category chem_link in the CHEM_LINK
category.
chem_link_chir_atom
Data items in the CHEM_LINK_CHIR_ATOM category enumerate the
atoms bonded to a chiral atom in a link between two
chemical components.
0
1
0
1
1
1
chem_link_chir_atomCategory
This property indicates that datablock
has a category element chem_link_chir_atom.
chem_link_chir_atomItem
Abstract Datatype property for chem_link_chir_atom items.
reference_to_chem_link_chir_atom
cross-reference to chem_link_chir_atom
1
2
This data item indicates whether the atom bonded to a chiral
atom is found in the first or the second of the two components
connected by the link.
chem_link_chir_atom.dev
The standard uncertainty (estimated standard deviation)
of the position of this atom from the plane defined by
all of the atoms in the plane.
chem_link_chir_atom.atom_id
The ID of an atom bonded to the chiral atom.
As this data item does not point to a specific atom in a
specific chemical component, it is not a child in the linkage
sense.
chem_link_chir_atom.chir_id
This data item is a pointer to attribute id in category chem_link_chir in the
CHEM_LINK_CHIR category.
chem_link_plane
Data items in the CHEM_LINK_PLANE category provide identifiers
for the planes in a link between two chemical components.
The atoms in the plane are specified in the CHEM_LINK_PLANE_ATOM
category.
0
1
0
1
1
1
chem_link_planeCategory
This property indicates that datablock
has a category element chem_link_plane.
chem_link_planeItem
Abstract Datatype property for chem_link_plane items.
reference_to_chem_link_plane
cross-reference to chem_link_plane
chem_link_plane.number_atoms_all
The total number of atoms in the plane.
chem_link_plane.number_atoms_nh
The number of non-hydrogen atoms in the plane.
chem_link_plane.id
The value of attribute id in category chem_link_plane must uniquely identify a record
in the CHEM_LINK_PLANE list.
chem_link_plane.link_id
This data item is a pointer to attribute id in category chem_link in the CHEM_LINK
category.
chem_link_plane_atom
Data items in the CHEM_LINK_PLANE_ATOM category enumerate the
atoms in a plane in a link between two chemical components.
0
1
1
1
chem_link_plane_atomCategory
This property indicates that datablock
has a category element chem_link_plane_atom.
chem_link_plane_atomItem
Abstract Datatype property for chem_link_plane_atom items.
reference_to_chem_link_plane_atom
cross-reference to chem_link_plane_atom
1
2
This data item indicates whether the atom in a plane is found in
the first or the second of the two components connected by the
link.
chem_link_plane_atom.atom_id
The ID of an atom involved in the plane.
As this data item does not point to a specific atom in a
specific chemical component, it is not a child in the linkage
sense.
chem_link_plane_atom.plane_id
This data item is a pointer to attribute id in category chem_link_plane in the
CHEM_LINK_PLANE category.
chem_link_tor
Data items in the CHEM_LINK_TOR category record details about
the torsion angles in a link between two chemical components.
As torsion angles can have more than one target value, the
target values are specified in the CHEM_LINK_TOR_VALUE category.
0
1
0
1
0
1
0
1
1
1
1
1
1
1
1
1
1
1
chem_link_torCategory
This property indicates that datablock
has a category element chem_link_tor.
chem_link_torItem
Abstract Datatype property for chem_link_tor items.
reference_to_chem_link_tor
cross-reference to chem_link_tor
1
2
This data item indicates whether atom 1 is found in the first
or the second of the two components connected by the link.
1
2
This data item indicates whether atom 2 is found in the first
or the second of the two components connected by the link.
1
2
This data item indicates whether atom 3 is found in the first
or the second of the two components connected by the link.
1
2
This data item indicates whether atom 4 is found in the first
or the second of the two components connected by the link.
chem_link_tor.atom_id_1
The ID of the first of the four atoms that define the torsion
angle.
As this data item does not point to a specific atom in a
specific chemical component, it is not a child in the linkage
sense.
chem_link_tor.atom_id_2
The ID of the second of the four atoms that define the torsion
angle.
As this data item does not point to a specific atom in a
specific chemical component, it is not a child in the linkage
sense.
chem_link_tor.atom_id_3
The ID of the third of the four atoms that define the torsion
angle.
As this data item does not point to a specific atom in a
specific chemical component, it is not a child in the linkage
sense.
chem_link_tor.atom_id_4
The ID of the fourth of the four atoms that define the torsion
angle.
As this data item does not point to a specific atom in a
specific chemical component, it is not a child in the linkage
sense.
chem_link_tor.id
The value of attribute id in category chem_link_tor must uniquely identify a
record in the CHEM_LINK_TOR list.
chem_link_tor.link_id
This data item is a pointer to attribute id in category chem_link in the CHEM_LINK
category.
chem_link_tor_value
Data items in the CHEM_LINK_TOR_VALUE category record details
about the target values for the torsion angles enumerated in the
CHEM_LINK_TOR list. Target values may be specified as angles
in degrees, as a distance between the first and fourth atoms, or
both.
1
1
1
1
0
1
0
1
1
chem_link_tor_valueCategory
This property indicates that datablock
has a category element chem_link_tor_value.
chem_link_tor_valueItem
Abstract Datatype property for chem_link_tor_value items.
reference_to_chem_link_tor_value
cross-reference to chem_link_tor_value
chem_link_tor_value.angle
A value that should be taken as a potential target value for the
torsion angle associated with the specified atoms, expressed in
degrees.
chem_link_tor_value.angle_esd
The standard uncertainty (estimated standard deviation)
of attribute angle in category chem_link_tor_value.
chem_link_tor_value.dist
A value that should be taken as a potential target value for the
torsion angle associated with the specified atoms, expressed as
the distance between the atoms specified by
_chem_link_tor.atom_id_1 and _chem_link_tor.atom_id_4 in the
referenced record in the CHEM_LINK_TOR list. Note that the
torsion angle cannot be fully specified by a distance (for
instance, a torsion angle of -60 degree will yield the same
distance as a 60 degree angle). However, the distance
specification can be useful for refinement in situations in
which the angle is already close to the desired value.
chem_link_tor_value.dist_esd
The standard uncertainty (estimated standard deviation)
of attribute dist in category chem_link_tor_value.
chem_link_tor_value.tor_id
This data item is a pointer to attribute id in category chem_link_tor in the
CHEM_LINK_TOR category.
chemical
Data items in the CHEMICAL category would not in general be
used in a macromolecular CIF. See instead the ENTITY data
items.
Data items in the CHEMICAL category record details about the
composition and chemical properties of the compounds. The
formula data items must agree with those that specify the
density, unit-cell and Z values.
Example 1 - based on data set 9597gaus of Alyea, Ferguson & Kannan
[Acta Cryst. (1996), C52, 765-767].
<PDBx:chemicalCategory>
<PDBx:chemical entry_id="9597gaus">
<PDBx:name_systematic>trans-bis(tricyclohexylphosphine)tetracarbonylmolybdenum(0)</PDBx:name_systematic>
</PDBx:chemical>
</PDBx:chemicalCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
chemicalCategory
This property indicates that datablock
has a category element chemical.
chemicalItem
Abstract Datatype property for chemical items.
reference_to_chemical
cross-reference to chemical
rm
ad
rmad
syn
unk
Necessary conditions for the assignment of
attribute absolute_configuration in category chemical are given by H. D. Flack and
G. Bernardinelli (1999, 2000).
Ref: Flack, H. D. & Bernardinelli, G. (1999). Acta Cryst. A55,
908-915. (http://www.iucr.org/paper?sh0129)
Flack, H. D. & Bernardinelli, G. (2000). J. Appl. Cryst.
33, 1143-1148. (http://www.iucr.org/paper?ks0021)
chemical.compound_source
Description of the source of the compound under study, or of the
parent molecule if a simple derivative is studied. This includes
the place of discovery for minerals or the actual source of a
natural product.
From Norilsk (USSR)
Extracted from the bark of Cinchona Naturalis
chemical.melting_point
The temperature in kelvins at which the crystalline solid changes
to a liquid.
chemical.melting_point_gt
A temperature in kelvins above
which the melting point (the temperature at which the
crystalline solid changes to a liquid) lies.
_chemical.melting_point_gt and _chemical.melting_point_lt
allow a range of temperatures to be given.
attribute melting_point in category chemical should always be used in preference
to these two items whenever possible.
chemical.melting_point_lt
A temperature in kelvins below which the melting point (the
temperature at which the crystalline solid changes to a liquid)
lies. _chemical.melting_point_gt and _chemical.melting_point_lt
allow a range of temperatures to be given.
attribute melting_point in category chemical should always be used in preference
to these two items whenever possible.
chemical.name_common
Trivial name by which the compound is commonly known.
1-bromoestradiol
chemical.name_mineral
Mineral name accepted by the International Mineralogical
Association. Use only for natural minerals. See also
attribute compound_source in category chemical.
chalcopyrite
chemical.name_structure_type
Commonly used structure-type name. Usually only applied to
minerals or inorganic compounds.
perovskite
sphalerite
A15
chemical.name_systematic
IUPAC or Chemical Abstracts full name of the compound.
1-bromoestra-1,3,5(10)-triene-3,17\b-diol
chemical.optical_rotation
The optical rotation in solution of the compound is
specified in the following format:
'[\a]^TEMP^~WAVE~ = SORT (c = CONC, SOLV)'
where:
TEMP is the temperature of the measurement in degrees
Celsius,
WAVE is an indication of the wavelength of the light
used for the measurement,
CONC is the concentration of the solution given as the
mass of the substance in g in 100 ml of solution,
SORT is the signed value (preceded by a + or a - sign)
of 100.\a/(l.c), where \a is the signed optical
rotation in degrees measured in a cell of length l in
dm and c is the value of CONC as defined above, and
SOLV is the chemical formula of the solvent.
[\a]^25^~D~ = +108 (c = 3.42, CHCl~3~)
chemical.properties_biological
A free-text description of the biological properties of the
material.
diverse biological activities including use as a
laxative and strong antibacterial activity against
S. aureus and weak activity against
cyclooxygenase-1 (COX-1)
antibiotic activity against Bacillus subtilis
(ATCC 6051) but no significant activity against
Candida albicans (ATCC 14053), Aspergillus flavus
(NRRL 6541) and Fusarium verticillioides (NRRL
25457)
weakly potent lipoxygenase nonredox inhibitor
no influenza A virus sialidase inhibitory and
plaque reduction activities
low toxicity against Drosophila melanogaster
chemical.properties_physical
A free-text description of the physical properties of the material.
air-sensitive
moisture-sensitive
hygroscopic
deliquescent
oxygen-sensitive
photo-sensitive
pyrophoric
semiconductor
ferromagnetic at low temperature
paramagnetic and thermochromic
chemical.temperature_decomposition
The temperature in kelvins at which the solid decomposes.
350
chemical.temperature_decomposition_esd
The estimated standard deviation of
attribute temperature_decomposition in category chemical.
chemical.temperature_decomposition_gt
A temperature in kelvins above which the solid is known to
decompose. attribute temperature_decomposition_gt in category chemical and
attribute temperature_decomposition_lt in category chemical allow
a range of temperatures to be given.
attribute temperature_decomposition in category chemical should always be used in
preference to these two items whenever possible.
350
chemical.temperature_decomposition_lt
A temperature in kelvins below which the solid is known to
decompose. attribute temperature_decomposition_gt in category chemical and
attribute temperature_decomposition_lt in category chemical allow
a range of temperatures to be given.
attribute temperature_decomposition in category chemical should always be used in
preference to these two items whenever possible.
350
chemical.temperature_sublimation
The temperature in kelvins at which the solid sublimes.
350
chemical.temperature_sublimation_esd
The estimated standard deviation of
attribute temperature_sublimation in category chemical.
chemical.temperature_sublimation_gt
A temperature in kelvins above which the solid is known to
sublime. attribute temperature_sublimation_gt in category chemical and
attribute temperature_sublimation_lt in category chemical allow a
range of temperatures to be given.
attribute temperature_sublimation in category chemical should always be used in
preference to these two items whenever possible.
350
chemical.temperature_sublimation_lt
A temperature in kelvins below which the solid is known to
sublime. attribute temperature_sublimation_gt in category chemical and
attribute temperature_sublimation_lt in category chemical allow a
range of temperatures to be given.
attribute temperature_sublimation in category chemical should always be used in
preference to these two items whenever possible.
350
chemical.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
chemical_conn_atom
Data items in the CHEMICAL_CONN_ATOM category would not, in
general, be used in a macromolecular CIF. See instead the
ENTITY data items.
Data items in the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND
categories record details about the two-dimensional (2D)
chemical structure of the molecular species. They allow
a 2D chemical diagram to be reconstructed for use in a
publication or in a database search for structural and
substructural relationships.
The CHEMICAL_CONN_ATOM data items provide information about the
chemical properties of the atoms in the structure. In cases
where crystallographic and molecular symmetry elements coincide,
they must also contain symmetry-generated atoms, so that the
CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND data items will always
describe a complete chemical entity.
Example 1 - based on data set DPTD of Yamin, Suwandi, Fun, Sivakumar &
bin Shawkataly [Acta Cryst. (1996), C52, 951-953].
<PDBx:chemical_conn_atomCategory>
<PDBx:chemical_conn_atom number="1">
<PDBx:NCA>1</PDBx:NCA>
<PDBx:NH>0</PDBx:NH>
<PDBx:display_x>.39</PDBx:display_x>
<PDBx:display_y>.81</PDBx:display_y>
<PDBx:type_symbol>S</PDBx:type_symbol>
</PDBx:chemical_conn_atom>
<PDBx:chemical_conn_atom number="2">
<PDBx:NCA>2</PDBx:NCA>
<PDBx:NH>0</PDBx:NH>
<PDBx:display_x>.39</PDBx:display_x>
<PDBx:display_y>.96</PDBx:display_y>
<PDBx:type_symbol>S</PDBx:type_symbol>
</PDBx:chemical_conn_atom>
<PDBx:chemical_conn_atom number="3">
<PDBx:NCA>3</PDBx:NCA>
<PDBx:NH>0</PDBx:NH>
<PDBx:display_x>.14</PDBx:display_x>
<PDBx:display_y>.88</PDBx:display_y>
<PDBx:type_symbol>N</PDBx:type_symbol>
</PDBx:chemical_conn_atom>
<PDBx:chemical_conn_atom number="4">
<PDBx:NCA>3</PDBx:NCA>
<PDBx:NH>0</PDBx:NH>
<PDBx:display_x>.33</PDBx:display_x>
<PDBx:display_y>.88</PDBx:display_y>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chemical_conn_atom>
<PDBx:chemical_conn_atom number="5">
<PDBx:NCA>2</PDBx:NCA>
<PDBx:NH>2</PDBx:NH>
<PDBx:display_x>.11</PDBx:display_x>
<PDBx:display_y>.96</PDBx:display_y>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chemical_conn_atom>
<PDBx:chemical_conn_atom number="6">
<PDBx:NCA>2</PDBx:NCA>
<PDBx:NH>2</PDBx:NH>
<PDBx:display_x>.03</PDBx:display_x>
<PDBx:display_y>.96</PDBx:display_y>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chemical_conn_atom>
<PDBx:chemical_conn_atom number="7">
<PDBx:NCA>2</PDBx:NCA>
<PDBx:NH>2</PDBx:NH>
<PDBx:display_x>.03</PDBx:display_x>
<PDBx:display_y>.80</PDBx:display_y>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chemical_conn_atom>
<PDBx:chemical_conn_atom number="8">
<PDBx:NCA>2</PDBx:NCA>
<PDBx:NH>2</PDBx:NH>
<PDBx:display_x>.11</PDBx:display_x>
<PDBx:display_y>.80</PDBx:display_y>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chemical_conn_atom>
<PDBx:chemical_conn_atom number="9">
<PDBx:NCA>1</PDBx:NCA>
<PDBx:NH>0</PDBx:NH>
<PDBx:display_x>.54</PDBx:display_x>
<PDBx:display_y>.81</PDBx:display_y>
<PDBx:type_symbol>S</PDBx:type_symbol>
</PDBx:chemical_conn_atom>
<PDBx:chemical_conn_atom number="10">
<PDBx:NCA>2</PDBx:NCA>
<PDBx:NH>0</PDBx:NH>
<PDBx:display_x>.54</PDBx:display_x>
<PDBx:display_y>.96</PDBx:display_y>
<PDBx:type_symbol>S</PDBx:type_symbol>
</PDBx:chemical_conn_atom>
<PDBx:chemical_conn_atom number="11">
<PDBx:NCA>3</PDBx:NCA>
<PDBx:NH>0</PDBx:NH>
<PDBx:display_x>.80</PDBx:display_x>
<PDBx:display_y>.88</PDBx:display_y>
<PDBx:type_symbol>N</PDBx:type_symbol>
</PDBx:chemical_conn_atom>
<PDBx:chemical_conn_atom number="12">
<PDBx:NCA>3</PDBx:NCA>
<PDBx:NH>0</PDBx:NH>
<PDBx:display_x>.60</PDBx:display_x>
<PDBx:display_y>.88</PDBx:display_y>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chemical_conn_atom>
<PDBx:chemical_conn_atom number="13">
<PDBx:NCA>2</PDBx:NCA>
<PDBx:NH>2</PDBx:NH>
<PDBx:display_x>.84</PDBx:display_x>
<PDBx:display_y>.96</PDBx:display_y>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chemical_conn_atom>
<PDBx:chemical_conn_atom number="14">
<PDBx:NCA>2</PDBx:NCA>
<PDBx:NH>2</PDBx:NH>
<PDBx:display_x>.91</PDBx:display_x>
<PDBx:display_y>.96</PDBx:display_y>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chemical_conn_atom>
<PDBx:chemical_conn_atom number="15">
<PDBx:NCA>2</PDBx:NCA>
<PDBx:NH>2</PDBx:NH>
<PDBx:display_x>.91</PDBx:display_x>
<PDBx:display_y>.80</PDBx:display_y>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chemical_conn_atom>
<PDBx:chemical_conn_atom number="16">
<PDBx:NCA>2</PDBx:NCA>
<PDBx:NH>2</PDBx:NH>
<PDBx:display_x>.84</PDBx:display_x>
<PDBx:display_y>.80</PDBx:display_y>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:chemical_conn_atom>
</PDBx:chemical_conn_atomCategory>
0
1
0
1
0
1
0
1
0
1
1
1
1
chemical_conn_atomCategory
This property indicates that datablock
has a category element chemical_conn_atom.
chemical_conn_atomItem
Abstract Datatype property for chemical_conn_atom items.
reference_to_chemical_conn_atom
cross-reference to chemical_conn_atom
chemical_conn_atom.NCA
The number of connected atoms excluding terminal hydrogen atoms.
chemical_conn_atom.NH
The total number of hydrogen atoms attached to this atom,
regardless of whether they are included in the refinement or
the ATOM_SITE list. This number is the same as
attribute attached_hydrogens in category atom_site only if none of the hydrogen
atoms appear in the ATOM_SITE list.
chemical_conn_atom.charge
The net integer charge assigned to this atom. This is the
formal charge assignment normally found in chemical diagrams.
for an ammonium nitrogen
1
for a chloride ion
-1
chemical_conn_atom.display_x
The 2D Cartesian x coordinate of the position of this atom in a
recognizable chemical diagram. The coordinate origin is at the
lower left corner, the x axis is horizontal and the y axis
is vertical. The coordinates must lie in the range 0.0 to 1.0.
These coordinates can be obtained from projections of a suitable
uncluttered view of the molecular structure.
chemical_conn_atom.display_y
The 2D Cartesian y coordinate of the position of this atom in a
recognizable chemical diagram. The coordinate origin is at the
lower left corner, the x axis is horizontal and the y axis
is vertical. The coordinates must lie in the range 0.0 to 1.0.
These coordinates can be obtained from projections of a suitable
uncluttered view of the molecular structure.
chemical_conn_atom.type_symbol
This data item is a pointer to attribute symbol in category atom_type in the
ATOM_TYPE category.
chemical_conn_atom.number
The chemical sequence number to be associated with this atom.
Within an ATOM_SITE list, this number must match one of
the attribute chemical_conn_number in category atom_site values.
chemical_conn_bond
Data items in the CHEMICAL_CONN_BOND category would not, in
general, be used in a macromolecular CIF. See instead the
ENTITY data items.
Data items in the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND
categories record details about the two-dimensional (2D)
chemical structure of the molecular species. They allow a
2D chemical diagram to be reconstructed for use in a
publication or in a database search for structural and
substructural relationships.
The CHEMICAL_CONN_BOND data items specify the connections
between the atoms in the CHEMICAL_CONN_ATOM list and the nature
of the chemical bond between these atoms.
Example 1 - based on data set DPTD of Yamin, Suwandi, Fun, Sivakumar &
bin Shawkataly [Acta Cryst. (1996), C52, 951-953].
<PDBx:chemical_conn_bondCategory>
<PDBx:chemical_conn_bond atom_1="4" atom_2="1">
<PDBx:type>doub</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="4" atom_2="3">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="4" atom_2="2">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="5" atom_2="3">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="6" atom_2="5">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="7" atom_2="6">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="8" atom_2="7">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="8" atom_2="3">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="10" atom_2="2">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="12" atom_2="9">
<PDBx:type>doub</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="12" atom_2="11">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="12" atom_2="10">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="13" atom_2="11">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="14" atom_2="13">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="15" atom_2="14">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="16" atom_2="15">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="16" atom_2="11">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="17" atom_2="5">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="18" atom_2="5">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="19" atom_2="6">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="20" atom_2="6">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="21" atom_2="7">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="22" atom_2="7">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="23" atom_2="8">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="24" atom_2="8">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="25" atom_2="13">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="26" atom_2="13">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="27" atom_2="14">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="28" atom_2="14">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="29" atom_2="15">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="30" atom_2="15">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="31" atom_2="16">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
<PDBx:chemical_conn_bond atom_1="32" atom_2="16">
<PDBx:type>sing</PDBx:type>
</PDBx:chemical_conn_bond>
</PDBx:chemical_conn_bondCategory>
0
1
1
1
chemical_conn_bondCategory
This property indicates that datablock
has a category element chemical_conn_bond.
chemical_conn_bondItem
Abstract Datatype property for chemical_conn_bond items.
reference_to_chemical_conn_bond
cross-reference to chemical_conn_bond
sing
doub
trip
quad
arom
poly
delo
pi
The chemical bond type associated with the connection between
the two sites attribute atom_1 in category chemical_conn_bond and
attribute atom_2 in category chemical_conn_bond.
chemical_conn_bond.atom_1
This data item is a pointer to attribute number in category chemical_conn_atom in the
CHEMICAL_CONN_ATOM category.
chemical_conn_bond.atom_2
This data item is a pointer to attribute number in category chemical_conn_atom in the
CHEMICAL_CONN_ATOM category.
chemical_formula
Data items in the CHEMICAL_FORMULA category would not, in
general, be used in a macromolecular CIF. See instead the
ENTITY data items.
Data items in the CHEMICAL_FORMULA category specify the
composition and chemical properties of the compound. The formula
data items must agree with those that specify the density,
unit-cell and Z values.
The following rules apply to the construction of the data items
_chemical_formula.analytical, _chemical_formula.structural and
attribute sum in category chemical_formula. For the data item
attribute moiety in category chemical_formula, the formula construction is broken up
into residues or moieties, i.e. groups of atoms that form a
molecular unit or molecular ion. The rules given below apply
within each moiety but different requirements apply to the way
that moieties are connected (see attribute moiety).
in category chemical_formula
(1) Only recognized element symbols may be used.
(2) Each element symbol is followed by a 'count' number. A count
of '1' may be omitted.
(3) A space or parenthesis must separate each cluster of (element
symbol + count).
(4) Where a group of elements is enclosed in parentheses, the
multiplier for the group must follow the closing parenthesis.
That is, all element and group multipliers are assumed to be
printed as subscripted numbers. (An exception to this rule
exists for attribute moiety in category chemical_formula formulae where pre- and
post-multipliers are permitted for molecular units.)
(5) Unless the elements are ordered in a manner that corresponds
to their chemical structure, as in
attribute structural in category chemical_formula, the order of the elements within
any group or moiety should be: C, then H, then the other
elements in alphabetical order of their symbol. This is the
'Hill' system used by Chemical Abstracts. This ordering is
used in _chemical_formula.moiety and _chemical_formula.sum.
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
<PDBx:chemical_formulaCategory>
<PDBx:chemical_formula entry_id="TOZ">
<PDBx:moiety>C18 H25 N O3</PDBx:moiety>
<PDBx:sum>C18 H25 N O3</PDBx:sum>
<PDBx:weight>303.40</PDBx:weight>
</PDBx:chemical_formula>
</PDBx:chemical_formulaCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
chemical_formulaCategory
This property indicates that datablock
has a category element chemical_formula.
chemical_formulaItem
Abstract Datatype property for chemical_formula items.
reference_to_chemical_formula
cross-reference to chemical_formula
chemical_formula.analytical
Formula determined by standard chemical analysis including trace
elements. See the CHEMICAL_FORMULA category description for
rules for writing chemical formulae. Parentheses are used only
for standard uncertainties (estimated standard deviations).
Fe2.45(2) Ni1.60(3) S4
chemical_formula.iupac
Formula expressed in conformance with IUPAC rules for inorganic
and metal-organic compounds where these conflict with the rules
for any other CHEMICAL_FORMULA entries. Typically used for
formatting a formula in accordance with journal rules. This
should appear in the data block in addition to the most
appropriate of the other CHEMICAL_FORMULA data names.
Ref: IUPAC (1990). Nomenclature of Inorganic Chemistry.
Oxford: Blackwell Scientific Publications.
[Co Re (C12 H22 P)2 (C O)6].0.5C H3 O H
chemical_formula.moiety
Formula with each discrete bonded residue or ion shown as a
separate moiety. See the CHEMICAL_FORMULA category description
for rules for writing chemical formulae. In addition to the
general formulae requirements, the following rules apply:
(1) Moieties are separated by commas ','.
(2) The order of elements within a moiety follows general rule
(5) in the CHEMICAL_FORMULA category description.
(3) Parentheses are not used within moieties but may surround
a moiety. Parentheses may not be nested.
(4) Charges should be placed at the end of the moiety. The
charge '+' or '-' may be preceded by a numerical multiplier
and should be separated from the last (element symbol +
count) by a space. Pre- or post-multipliers may be used for
individual moieties.
C7 H4 Cl Hg N O3 S
C12 H17 N4 O S 1+, C6 H2 N3 O7 1-
C12 H16 N2 O6, 5(H2 O1)
(Cd 2+)3, (C6 N6 Cr 3-)2, 2(H2 O)
chemical_formula.structural
See the CHEMICAL_FORMULA category description for the rules for
writing chemical formulae for inorganics, organometallics, metal
complexes etc., in which bonded groups are preserved as
discrete entities within parentheses, with post-multipliers as
required. The order of the elements should give as much
information as possible about the chemical structure.
Parentheses may be used and nested as required. This formula
should correspond to the structure as actually reported, i.e.
trace elements not included in atom-type and atom-site data
should not be included in this formula (see also
attribute analytical) in category chemical_formula.
Ca ((Cl O3)2 O)2 (H2 O)6
(Pt (N H3)2 (C5 H7 N3 O)2) (Cl O4)2
chemical_formula.sum
See the CHEMICAL_FORMULA category description for the rules
for writing chemical formulae in which all discrete bonded
residues and ions are summed over the constituent elements,
following the ordering given in general rule (5) in the
CHEMICAL_FORMULA category description. Parentheses are not
normally used.
C18 H19 N7 O8 S
chemical_formula.weight
Formula mass in daltons. This mass should correspond to the
formulae given under attribute structural,
in category chemical_formula _chemical_formula.moiety or _chemical_formula.sum and,
together with the Z value and cell parameters, should
yield the density given as attribute density_diffrn in category exptl_crystal.
chemical_formula.weight_meas
Formula mass in daltons measured by a non-diffraction experiment.
chemical_formula.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
citation
Data items in the CITATION category record details about the
literature cited as being relevant to the contents of the data
block.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:citationCategory>
<PDBx:citation id="primary">
<PDBx:book_id_ISBN></PDBx:book_id_ISBN>
<PDBx:book_publisher></PDBx:book_publisher>
<PDBx:book_title></PDBx:book_title>
<PDBx:coordinate_linkage>yes</PDBx:coordinate_linkage>
<PDBx:country>US</PDBx:country>
<PDBx:details> The publication that directly relates to this coordinate
set.</PDBx:details>
<PDBx:journal_abbrev>J. Biol. Chem.</PDBx:journal_abbrev>
<PDBx:journal_id_ASTM>HBCHA3</PDBx:journal_id_ASTM>
<PDBx:journal_id_CSD>071</PDBx:journal_id_CSD>
<PDBx:journal_id_ISSN>0021-9258</PDBx:journal_id_ISSN>
<PDBx:journal_issue></PDBx:journal_issue>
<PDBx:journal_volume>265</PDBx:journal_volume>
<PDBx:page_first>14209</PDBx:page_first>
<PDBx:page_last>14219</PDBx:page_last>
<PDBx:title> Crystallographic analysis of a complex between human
immunodeficiency virus type 1 protease and acetyl-pepstatin
at 2.0-Angstroms resolution.</PDBx:title>
<PDBx:year>1990</PDBx:year>
</PDBx:citation>
<PDBx:citation id="2">
<PDBx:book_id_ISBN></PDBx:book_id_ISBN>
<PDBx:book_publisher></PDBx:book_publisher>
<PDBx:book_title></PDBx:book_title>
<PDBx:coordinate_linkage>no</PDBx:coordinate_linkage>
<PDBx:country>UK</PDBx:country>
<PDBx:details> Determination of the structure of the unliganded enzyme.</PDBx:details>
<PDBx:journal_abbrev>Nature</PDBx:journal_abbrev>
<PDBx:journal_id_ASTM>NATUAS</PDBx:journal_id_ASTM>
<PDBx:journal_id_CSD>006</PDBx:journal_id_CSD>
<PDBx:journal_id_ISSN>0028-0836</PDBx:journal_id_ISSN>
<PDBx:journal_issue></PDBx:journal_issue>
<PDBx:journal_volume>337</PDBx:journal_volume>
<PDBx:page_first>615</PDBx:page_first>
<PDBx:page_last>619</PDBx:page_last>
<PDBx:title> Three-dimensional structure of aspartyl-protease from human
immunodeficiency virus HIV-1.</PDBx:title>
<PDBx:year>1989</PDBx:year>
</PDBx:citation>
<PDBx:citation id="3">
<PDBx:book_id_ISBN></PDBx:book_id_ISBN>
<PDBx:book_publisher></PDBx:book_publisher>
<PDBx:book_title></PDBx:book_title>
<PDBx:coordinate_linkage>no</PDBx:coordinate_linkage>
<PDBx:country>US</PDBx:country>
<PDBx:details> Crystallization of the unliganded enzyme.</PDBx:details>
<PDBx:journal_abbrev>J. Biol. Chem.</PDBx:journal_abbrev>
<PDBx:journal_id_ASTM>HBCHA3</PDBx:journal_id_ASTM>
<PDBx:journal_id_CSD>071</PDBx:journal_id_CSD>
<PDBx:journal_id_ISSN>0021-9258</PDBx:journal_id_ISSN>
<PDBx:journal_issue></PDBx:journal_issue>
<PDBx:journal_volume>264</PDBx:journal_volume>
<PDBx:page_first>1919</PDBx:page_first>
<PDBx:page_last>1921</PDBx:page_last>
<PDBx:title> Crystallization of the aspartylprotease from human
immunodeficiency virus, HIV-1.</PDBx:title>
<PDBx:year>1989</PDBx:year>
</PDBx:citation>
<PDBx:citation id="4">
<PDBx:book_id_ISBN></PDBx:book_id_ISBN>
<PDBx:book_publisher></PDBx:book_publisher>
<PDBx:book_title></PDBx:book_title>
<PDBx:coordinate_linkage>no</PDBx:coordinate_linkage>
<PDBx:country>US</PDBx:country>
<PDBx:details> Expression and purification of the enzyme.</PDBx:details>
<PDBx:journal_abbrev>J. Biol. Chem.</PDBx:journal_abbrev>
<PDBx:journal_id_ASTM>HBCHA3</PDBx:journal_id_ASTM>
<PDBx:journal_id_CSD>071</PDBx:journal_id_CSD>
<PDBx:journal_id_ISSN>0021-9258</PDBx:journal_id_ISSN>
<PDBx:journal_issue></PDBx:journal_issue>
<PDBx:journal_volume>264</PDBx:journal_volume>
<PDBx:page_first>2307</PDBx:page_first>
<PDBx:page_last>2312</PDBx:page_last>
<PDBx:title> Human immunodeficiency virus protease. Bacterial expression
and characterization of the purified aspartic protease.</PDBx:title>
<PDBx:year>1989</PDBx:year>
</PDBx:citation>
</PDBx:citationCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
citationCategory
This property indicates that datablock
has a category element citation.
citationItem
Abstract Datatype property for citation items.
reference_to_citation
cross-reference to citation
citation.abstract
Abstract for the citation. This is used most when the
citation is extracted from a bibliographic database that
contains full text or abstract information.
citation.abstract_id_CAS
The Chemical Abstracts Service (CAS) abstract identifier;
relevant for journal articles.
citation.book_id_ISBN
The International Standard Book Number (ISBN) code assigned to
the book cited; relevant for books or book chapters.
citation.book_publisher
The name of the publisher of the citation; relevant
for books or book chapters.
John Wiley and Sons
citation.book_publisher_city
The location of the publisher of the citation; relevant
for books or book chapters.
London
citation.book_title
The title of the book in which the citation appeared; relevant
for books or book chapters.
no
n
yes
y
attribute coordinate_linkage in category citation states whether this citation
is concerned with precisely the set of coordinates given in the
data block. If, for instance, the publication described the same
structure, but the coordinates had undergone further refinement
prior to the creation of the data block, the value of this data
item would be 'no'.
citation.country
The country of publication; relevant for books
and book chapters.
citation.database_id_CSD
Identifier ('refcode') of the database record in the Cambridge
Structural Database that contains details of the cited structure.
LEKKUH
citation.database_id_Medline
Accession number used by Medline to categorize a specific
bibliographic entry.
89064067
citation.details
A description of special aspects of the relationship
of the contents of the data block to the literature item cited.
citation relates to this precise
coordinate set
citation relates to earlier low-resolution
structure
citation relates to further refinement of
structure reported in citation 2
citation.journal_abbrev
Abbreviated name of the cited journal as given in the
Chemical Abstracts Service Source Index.
J. Mol. Biol.
citation.journal_full
Full name of the cited journal; relevant for journal articles.
Journal of Molecular Biology
citation.journal_id_ASTM
The American Society for Testing and Materials (ASTM) code
assigned to the journal cited (also referred to as the CODEN
designator of the Chemical Abstracts Service); relevant for
journal articles.
citation.journal_id_CSD
The Cambridge Structural Database (CSD) code assigned to the
journal cited; relevant for journal articles. This is also the
system used at the Protein Data Bank (PDB).
0070
citation.journal_id_ISSN
The International Standard Serial Number (ISSN) code assigned to
the journal cited; relevant for journal articles.
citation.journal_issue
Issue number of the journal cited; relevant for journal
articles.
2
citation.journal_volume
Volume number of the journal cited; relevant for journal
articles.
174
citation.language
Language in which the cited article is written.
German
citation.page_first
The first page of the citation; relevant for journal
articles, books and book chapters.
citation.page_last
The last page of the citation; relevant for journal
articles, books and book chapters.
citation.pdbx_database_id_DOI
Document Object Identifier used by doi.org to uniquely
specify bibliographic entry.
DOI:10.2345/S1384107697000225
citation.pdbx_database_id_PubMed
Ascession number used by PubMed to categorize a specific
bibliographic entry.
12627512
citation.title
The title of the citation; relevant for journal articles, books
and book chapters.
Structure of diferric duck ovotransferrin
at 2.35 \%A resolution.
Y
N
Flag to indicate that this citation will not be published.
citation.year
The year of the citation; relevant for journal articles, books
and book chapters.
1984
citation.id
The value of attribute id in category citation must uniquely identify a record in the
CITATION list.
The attribute id in category citation 'primary' should be used to indicate the
citation that the author(s) consider to be the most pertinent to
the contents of the data block.
Note that this item need not be a number; it can be any unique
identifier.
primary
1
2
citation_author
Data items in the CITATION_AUTHOR category record details
about the authors associated with the citations in the
CITATION list.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:citation_authorCategory>
<PDBx:citation_author citation_id="primary" name="Fitzgerald, P.M.D." ordinal="1"></PDBx:citation_author>
<PDBx:citation_author citation_id="primary" name="McKeever, B.M." ordinal="2"></PDBx:citation_author>
<PDBx:citation_author citation_id="primary" name="Van Middlesworth, J.F." ordinal="3"></PDBx:citation_author>
<PDBx:citation_author citation_id="primary" name="Springer, J.P." ordinal="4"></PDBx:citation_author>
<PDBx:citation_author citation_id="primary" name="Heimbach, J.C." ordinal="5"></PDBx:citation_author>
<PDBx:citation_author citation_id="primary" name="Leu, C.-T." ordinal="6"></PDBx:citation_author>
<PDBx:citation_author citation_id="primary" name="Herber, W.K." ordinal="7"></PDBx:citation_author>
<PDBx:citation_author citation_id="primary" name="Dixon, R.A.F." ordinal="8"></PDBx:citation_author>
<PDBx:citation_author citation_id="primary" name="Darke, P.L." ordinal="9"></PDBx:citation_author>
<PDBx:citation_author citation_id="2" name="Navia, M.A." ordinal="1"></PDBx:citation_author>
<PDBx:citation_author citation_id="2" name="Fitzgerald, P.M.D." ordinal="2"></PDBx:citation_author>
<PDBx:citation_author citation_id="2" name="McKeever, B.M." ordinal="3"></PDBx:citation_author>
<PDBx:citation_author citation_id="2" name="Leu, C.-T." ordinal="4"></PDBx:citation_author>
<PDBx:citation_author citation_id="2" name="Heimbach, J.C." ordinal="5"></PDBx:citation_author>
<PDBx:citation_author citation_id="2" name="Herber, W.K." ordinal="6"></PDBx:citation_author>
<PDBx:citation_author citation_id="2" name="Sigal, I.S." ordinal="7"></PDBx:citation_author>
<PDBx:citation_author citation_id="2" name="Darke, P.L." ordinal="8"></PDBx:citation_author>
<PDBx:citation_author citation_id="2" name="Springer, J.P." ordinal="9"></PDBx:citation_author>
<PDBx:citation_author citation_id="3" name="McKeever, B.M." ordinal="1"></PDBx:citation_author>
<PDBx:citation_author citation_id="3" name="Navia, M.A." ordinal="2"></PDBx:citation_author>
<PDBx:citation_author citation_id="3" name="Fitzgerald, P.M.D." ordinal="3"></PDBx:citation_author>
<PDBx:citation_author citation_id="3" name="Springer, J.P." ordinal="4"></PDBx:citation_author>
<PDBx:citation_author citation_id="3" name="Leu, C.-T." ordinal="5"></PDBx:citation_author>
<PDBx:citation_author citation_id="3" name="Heimbach, J.C." ordinal="6"></PDBx:citation_author>
<PDBx:citation_author citation_id="3" name="Herber, W.K." ordinal="7"></PDBx:citation_author>
<PDBx:citation_author citation_id="3" name="Sigal, I.S." ordinal="8"></PDBx:citation_author>
<PDBx:citation_author citation_id="3" name="Darke, P.L." ordinal="9"></PDBx:citation_author>
<PDBx:citation_author citation_id="4" name="Darke, P.L." ordinal="1"></PDBx:citation_author>
<PDBx:citation_author citation_id="4" name="Leu, C.-T." ordinal="2"></PDBx:citation_author>
<PDBx:citation_author citation_id="4" name="Davis, L.J." ordinal="3"></PDBx:citation_author>
<PDBx:citation_author citation_id="4" name="Heimbach, J.C." ordinal="4"></PDBx:citation_author>
<PDBx:citation_author citation_id="4" name="Diehl, R.E." ordinal="5"></PDBx:citation_author>
<PDBx:citation_author citation_id="4" name="Hill, W.S." ordinal="6"></PDBx:citation_author>
<PDBx:citation_author citation_id="4" name="Dixon, R.A.F." ordinal="7"></PDBx:citation_author>
<PDBx:citation_author citation_id="4" name="Sigal, I.S." ordinal="8"></PDBx:citation_author>
</PDBx:citation_authorCategory>
1
1
1
citation_authorCategory
This property indicates that datablock
has a category element citation_author.
citation_authorItem
Abstract Datatype property for citation_author items.
reference_to_citation_author
cross-reference to citation_author
citation_author.citation_id
This data item is a pointer to attribute id in category citation in the CITATION
category.
citation_author.name
Name of an author of the citation; relevant for journal
articles, books and book chapters.
The family name(s), followed by a comma and including any
dynastic components, precedes the first name(s) or initial(s).
Bleary, Percival R.
O'Neil, F.K.
Van den Bossche, G.
Yang, D.-L.
Simonov, Yu.A
citation_author.ordinal
This data item defines the order of the author's name in the
list of authors of a citation.
citation_editor
Data items in the CITATION_EDITOR category record details
about the editors associated with the books or book chapters
cited in the CITATION list.
Example 1 - hypothetical example.
<PDBx:citation_editorCategory>
<PDBx:citation_editor citation_id="5" name="McKeever, B.M."></PDBx:citation_editor>
<PDBx:citation_editor citation_id="5" name="Navia, M.A."></PDBx:citation_editor>
<PDBx:citation_editor citation_id="5" name="Fitzgerald, P.M.D."></PDBx:citation_editor>
<PDBx:citation_editor citation_id="5" name="Springer, J.P."></PDBx:citation_editor>
</PDBx:citation_editorCategory>
0
1
1
1
citation_editorCategory
This property indicates that datablock
has a category element citation_editor.
citation_editorItem
Abstract Datatype property for citation_editor items.
reference_to_citation_editor
cross-reference to citation_editor
citation_editor.ordinal
This data item defines the order of the editor's name in the
list of editors of a citation.
citation_editor.citation_id
This data item is a pointer to attribute id in category citation in the CITATION
category.
citation_editor.name
Names of an editor of the citation; relevant for books and
book chapters.
The family name(s), followed by a comma and including any
dynastic components, precedes the first name(s) or initial(s).
Bleary, Percival R.
O'Neil, F.K.
Van den Bossche, G.
Yang, D.-L.
Simonov, Yu.A
computing
Data items in the COMPUTING category record details about the
computer programs used in the crystal structure analysis.
Data items in this category would not, in general, be used in
a macromolecular CIF. The category SOFTWARE, which allows
a more detailed description of computer programs and
their attributes to be given, would be used instead.
Example 1 - Rodr\'iguez-Romera, Ruiz-P\'erez & Solans [Acta
Cryst. (1996), C52, 1415-1417].
<PDBx:computingCategory>
<PDBx:computing entry_id="1ABC">
<PDBx:cell_refinement>CAD-4 (Enraf-Nonius, 1989)</PDBx:cell_refinement>
<PDBx:data_collection>CAD-4 (Enraf-Nonius, 1989)</PDBx:data_collection>
<PDBx:data_reduction>CFEO (Solans, 1978)</PDBx:data_reduction>
<PDBx:molecular_graphics>ORTEPII (Johnson, 1976)</PDBx:molecular_graphics>
<PDBx:publication_material>PARST (Nardelli, 1983)</PDBx:publication_material>
<PDBx:structure_refinement>SHELXL93 (Sheldrick, 1993)</PDBx:structure_refinement>
<PDBx:structure_solution>SHELXS86 (Sheldrick, 1990)</PDBx:structure_solution>
</PDBx:computing>
</PDBx:computingCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
computingCategory
This property indicates that datablock
has a category element computing.
computingItem
Abstract Datatype property for computing items.
reference_to_computing
cross-reference to computing
computing.cell_refinement
Software used for cell refinement.
Give the program or package name and a brief reference.
CAD4 (Enraf-Nonius, 1989)
computing.data_collection
Software used for data collection.
Give the program or package name and a brief reference.
CAD4 (Enraf-Nonius, 1989)
computing.data_reduction
Software used for data reduction.
Give the program or package name and a brief reference.
DIFDAT, SORTRF, ADDREF (Hall & Stewart, 1990)
computing.molecular_graphics
Software used for molecular graphics.
Give the program or package name and a brief reference.
FRODO (Jones, 1986), ORTEP (Johnson, 1965)
computing.pdbx_data_reduction_ds
Program/package name for data reduction/data scaling
computing.pdbx_data_reduction_ii
Program/package name for data reduction/intensity integration software
computing.pdbx_structure_refinement_method
Program/package name for structure refinement method.
computing.publication_material
Software used for generating material for publication.
Give the program or package name and a brief reference.
computing.structure_refinement
Software used for refinement of the structure.
Give the program or package name and a brief reference.
SHELX85 (Sheldrick, 1985)
X-PLOR (Brunger, 1992)
computing.structure_solution
Software used for solution of the structure.
Give the program or package name and a brief reference.
SHELX85 (Sheldrick, 1985)
computing.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
database
Data items in the DATABASE category have been superseded by
data items in the DATABASE_2 category. They are included
here only for compliance with older CIFs.
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
databaseCategory
This property indicates that datablock
has a category element database.
databaseItem
Abstract Datatype property for database items.
reference_to_database
cross-reference to database
database.CSD_history
A history of changes made by the Cambridge Crystallographic Data
Centre and incorporated into the Cambridge Structural Database
(CSD).
database.code_CAS
The code assigned by Chemical Abstracts.
database.code_CSD
The code assigned by the Cambridge Structural Database.
database.code_ICSD
The code assigned by the Inorganic Crystal Structure
Database.
database.code_MDF
The code assigned by the Metals Data File.
database.code_NBS
The code assigned by the NBS (NIST) Crystal Data Database.
database.code_PDB
The code assigned by the Protein Data Bank.
database.code_PDF
The code assigned by the Powder Diffraction File (JCPDS/ICDD).
database.code_depnum_ccdc_archive
Deposition numbers assigned by the Cambridge Crystallographic
Data Centre (CCDC) to files containing structural information
archived by the CCDC.
database.code_depnum_ccdc_fiz
Deposition numbers assigned by the Fachinformationszentrum
Karlsruhe (FIZ) to files containing structural information
archived by the Cambridge Crystallographic Data Centre (CCDC).
database.code_depnum_ccdc_journal
Deposition numbers assigned by various journals to files
containing structural information archived by the Cambridge
Crystallographic Data Centre (CCDC).
database.journal_ASTM
The ASTM CODEN designator for a journal as given in the Chemical
Source List maintained by the Chemical Abstracts Service.
database.journal_CSD
The journal code used in the Cambridge Structural Database.
database.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
database_2
Data items in the DATABASE_2 category record details about the
database identifiers of the data block.
These data items are assigned by database managers and should
only appear in a data block if they originate from that source.
The name of this category, DATABASE_2, arose because the
category name DATABASE was already in use in the core CIF
dictionary, but was used differently from the way it needed
to be used in the mmCIF dictionary. Since CIF data names
cannot be changed once they have been adopted, a new category
had to be created.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:database_2Category>
<PDBx:database_2 database_code="5HVP" database_id="PDB"></PDBx:database_2>
</PDBx:database_2Category>
1
1
database_2Category
This property indicates that datablock
has a category element database_2.
database_2Item
Abstract Datatype property for database_2 items.
reference_to_database_2
cross-reference to database_2
database_2.database_code
The code assigned by the database identified in
attribute database_id in category database_2.
1ABC
ABCDEF
CAS
CSD
ICSD
MDF
NDB
NBS
PDB
PDF
RCSB
EBI
BMRB
An abbreviation that identifies the database.
database_PDB_caveat
Data items in the DATABASE_PDB_CAVEAT category record details
about features of the data block flagged as 'caveats' by the
Protein Data Bank (PDB).
These data items are included only for consistency with PDB
format files. They should appear in a data block only if that
data block was created by reformatting a PDB format file.
Example 1 - hypothetical example.
<PDBx:database_PDB_caveatCategory>
<PDBx:database_PDB_caveat id="1">
<PDBx:text> THE CRYSTAL TRANSFORMATION IS IN ERROR BUT IS</PDBx:text>
</PDBx:database_PDB_caveat>
<PDBx:database_PDB_caveat id="2">
<PDBx:text> UNCORRECTABLE AT THIS TIME</PDBx:text>
</PDBx:database_PDB_caveat>
</PDBx:database_PDB_caveatCategory>
0
1
1
database_PDB_caveatCategory
This property indicates that datablock
has a category element database_PDB_caveat.
database_PDB_caveatItem
Abstract Datatype property for database_PDB_caveat items.
reference_to_database_PDB_caveat
cross-reference to database_PDB_caveat
database_PDB_caveat.text
The full text of the PDB caveat record.
database_PDB_caveat.id
A unique identifier for the PDB caveat record.
database_PDB_matrix
The DATABASE_PDB_MATRIX category provides placeholders for
transformation matrices and vectors used by the Protein Data
Bank (PDB).
These data items are included only for consistency with older
PDB format files. They should appear in a data block only if
that data block was created by reformatting a PDB format file.
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
database_PDB_matrixCategory
This property indicates that datablock
has a category element database_PDB_matrix.
database_PDB_matrixItem
Abstract Datatype property for database_PDB_matrix items.
reference_to_database_PDB_matrix
cross-reference to database_PDB_matrix
database_PDB_matrix.origx11
The [1][1] element of the PDB ORIGX matrix.
database_PDB_matrix.origx12
The [1][2] element of the PDB ORIGX matrix.
database_PDB_matrix.origx13
The [1][3] element of the PDB ORIGX matrix.
database_PDB_matrix.origx21
The [2][1] element of the PDB ORIGX matrix.
database_PDB_matrix.origx22
The [2][2] element of the PDB ORIGX matrix.
database_PDB_matrix.origx23
The [2][3] element of the PDB ORIGX matrix.
database_PDB_matrix.origx31
The [3][1] element of the PDB ORIGX matrix.
database_PDB_matrix.origx32
The [3][2] element of the PDB ORIGX matrix.
database_PDB_matrix.origx33
The [3][3] element of the PDB ORIGX matrix.
database_PDB_matrix.origx_vector1
The [1] element of the PDB ORIGX vector.
database_PDB_matrix.origx_vector2
The [2] element of the PDB ORIGX vector.
database_PDB_matrix.origx_vector3
The [3] element of the PDB ORIGX vector.
database_PDB_matrix.scale11
The [1][1] element of the PDB SCALE matrix.
database_PDB_matrix.scale12
The [1][2] element of the PDB SCALE matrix.
database_PDB_matrix.scale13
The [1][3] element of the PDB SCALE matrix.
database_PDB_matrix.scale21
The [2][1] element of the PDB SCALE matrix.
database_PDB_matrix.scale22
The [2][2] element of the PDB SCALE matrix.
database_PDB_matrix.scale23
The [2][3] element of the PDB SCALE matrix.
database_PDB_matrix.scale31
The [3][1] element of the PDB SCALE matrix.
database_PDB_matrix.scale32
The [3][2] element of the PDB SCALE matrix.
database_PDB_matrix.scale33
The [3][3] element of the PDB SCALE matrix.
database_PDB_matrix.scale_vector1
The [1] element of the PDB SCALE vector.
database_PDB_matrix.scale_vector2
The [2] element of the PDB SCALE vector.
database_PDB_matrix.scale_vector3
The [3] element of the PDB SCALE vector.
database_PDB_matrix.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
database_PDB_remark
Data items in the DATABASE_PDB_REMARK category record details
about the data block as archived by the Protein Data Bank (PDB).
Some data appearing in PDB REMARK records can be
algorithmically extracted into the appropriate data items
in the data block.
These data items are included only for consistency with older
PDB format files. They should appear in a data block only if
that data block was created by reformatting a PDB format file.
NOTE: These remark records in this category are not uniformly
annotated by the PDB and may not be consistent with
nomenclature or labeling used in the entry.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:database_PDB_remarkCategory>
<PDBx:database_PDB_remark id="3">
<PDBx:text> REFINEMENT. BY THE RESTRAINED LEAST-SQUARES PROCEDURE OF J.
KONNERT AND W. HENDRICKSON (PROGRAM *PROLSQ*). THE R
VALUE IS 0.176 FOR 12901 REFLECTIONS IN THE RESOLUTION
RANGE 8.0 TO 2.0 ANGSTROMS WITH I .GT. SIGMA(I).
RMS DEVIATIONS FROM IDEAL VALUES (THE VALUES OF
SIGMA, IN PARENTHESES, ARE THE INPUT ESTIMATED
STANDARD DEVIATIONS THAT DETERMINE THE RELATIVE
WEIGHTS OF THE CORRESPONDING RESTRAINTS)
DISTANCE RESTRAINTS (ANGSTROMS)
BOND DISTANCE 0.018(0.020)
ANGLE DISTANCE 0.038(0.030)
PLANAR 1-4 DISTANCE 0.043(0.040)
PLANE RESTRAINT (ANGSTROMS) 0.015(0.020)
CHIRAL-CENTER RESTRAINT (ANGSTROMS**3) 0.177(0.150)
NON-BONDED CONTACT RESTRAINTS (ANGSTROMS)
SINGLE TORSION CONTACT 0.216(0.500)
MULTIPLE TORSION CONTACT 0.207(0.500)
POSSIBLE HYDROGEN BOND 0.245(0.500)
CONFORMATIONAL TORSION ANGLE RESTRAINT (DEGREES)
PLANAR (OMEGA) 2.6(3.0)
STAGGERED 17.4(15.0)
ORTHONORMAL 18.1(20.0)</PDBx:text>
</PDBx:database_PDB_remark>
<PDBx:database_PDB_remark id="4">
<PDBx:text> THE TWO CHAINS OF THE DIMERIC ENZYME HAS BEEN ASSIGNED THE
THE CHAIN INDICATORS *A* AND *B*.</PDBx:text>
</PDBx:database_PDB_remark>
</PDBx:database_PDB_remarkCategory>
0
1
1
database_PDB_remarkCategory
This property indicates that datablock
has a category element database_PDB_remark.
database_PDB_remarkItem
Abstract Datatype property for database_PDB_remark items.
reference_to_database_PDB_remark
cross-reference to database_PDB_remark
database_PDB_remark.text
The full text of the PDB remark record.
database_PDB_remark.id
A unique identifier for the PDB remark record.
database_PDB_rev
Data items in the DATABASE_PDB_REV category record details
about the history of the data block as archived by the Protein
Data Bank (PDB).
These data items are assigned by the PDB database managers and
should only appear in a data block if they originate from that
source.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:database_PDB_revCategory>
<PDBx:database_PDB_rev num="1">
<PDBx:author_name>Fitzgerald, Paula M.D</PDBx:author_name>
<PDBx:date>1991-10-15</PDBx:date>
<PDBx:date_original>1990-04-30</PDBx:date_original>
<PDBx:mod_type>0</PDBx:mod_type>
<PDBx:status>full release</PDBx:status>
</PDBx:database_PDB_rev>
</PDBx:database_PDB_revCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
database_PDB_revCategory
This property indicates that datablock
has a category element database_PDB_rev.
database_PDB_revItem
Abstract Datatype property for database_PDB_rev items.
reference_to_database_PDB_rev
cross-reference to database_PDB_rev
database_PDB_rev.author_name
The name of the person responsible for submitting this revision
to the PDB.
The family name(s) followed by a comma precedes the first
name(s) or initial(s).
Bleary, Percival R.
O'Neil, F.K.
Van den Bossche, G.
Yang, D.-L.
Simonov, Yu.A
database_PDB_rev.date
Date the PDB revision took place. Taken from the REVDAT record.
database_PDB_rev.date_original
Date the entry first entered the PDB database in the form
yyyy-mm-dd. Taken from the PDB HEADER record.
1980-08-21
0
1
2
3
4
5
Taken from the REVDAT record. Refer to the Protein Data Bank
format description at
http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html
for details.
database_PDB_rev.replaced_by
The PDB code for a subsequent PDB entry that replaced the
PDB file corresponding to this data block.
database_PDB_rev.replaces
The PDB code for a previous PDB entry that was replaced by
the PDB file corresponding to this data block.
in preparation
prerelease
full release
obsolete
The status of this revision.
database_PDB_rev.num
The value of attribute num in category database_PDB_rev must uniquely and
sequentially identify a record in the DATABASE_PDB_REV list.
Note that this item must be a number and that modification
numbers are assigned in increasing numerical order.
database_PDB_rev_record
Data items in the DATABASE_PDB_REV_RECORD category record
details about specific record types that were changed in a
given revision of a PDB entry.
These data items are assigned by the PDB database managers and
should only appear in a data block if they originate from that
source.
Example 1 - hypothetical example.
<PDBx:database_PDB_rev_recordCategory>
<PDBx:database_PDB_rev_record rev_num="1" type="CONECT">
<PDBx:details> Error fix - incorrect connection between
atoms 2312 and 2317</PDBx:details>
</PDBx:database_PDB_rev_record>
<PDBx:database_PDB_rev_record rev_num="2" type="MATRIX">
<PDBx:details>For consistency with 1995-08-04 style-guide</PDBx:details>
</PDBx:database_PDB_rev_record>
<PDBx:database_PDB_rev_record rev_num="3" type="ORIGX">
<PDBx:details>Based on new data from author</PDBx:details>
</PDBx:database_PDB_rev_record>
</PDBx:database_PDB_rev_recordCategory>
0
1
1
1
database_PDB_rev_recordCategory
This property indicates that datablock
has a category element database_PDB_rev_record.
database_PDB_rev_recordItem
Abstract Datatype property for database_PDB_rev_record items.
reference_to_database_PDB_rev_record
cross-reference to database_PDB_rev_record
database_PDB_rev_record.details
A description of special aspects of the revision of records in
this PDB entry.
Based on new data from author
For consistency with 1995-08-04 style-guide
For consistency with structural class
database_PDB_rev_record.rev_num
This data item is a pointer to attribute num in category database_PDB_rev in the
DATABASE_PDB_REV category.
database_PDB_rev_record.type
The types of records that were changed in this revision to a
PDB entry.
CRYST1
SCALE
MTRIX
ATOM
HETATM
database_PDB_tvect
The DATABASE_PDB_TVECT category provides placeholders for
the TVECT matrices and vectors used by the Protein Data
Bank (PDB).
These data items are included only for consistency with older
PDB format files. They should appear in a data block only if
the data block was created by reformatting a PDB format file.
0
1
0
1
0
1
0
1
1
database_PDB_tvectCategory
This property indicates that datablock
has a category element database_PDB_tvect.
database_PDB_tvectItem
Abstract Datatype property for database_PDB_tvect items.
reference_to_database_PDB_tvect
cross-reference to database_PDB_tvect
database_PDB_tvect.details
A description of special aspects of this TVECT.
database_PDB_tvect.vector1
The [1] element of the PDB TVECT vector.
database_PDB_tvect.vector2
The [2] element of the PDB TVECT vector.
database_PDB_tvect.vector3
The [3] element of the PDB TVECT vector.
database_PDB_tvect.id
The value of attribute id in category database_PDB_tvect must uniquely identify a
record in the DATABASE_PDB_TVECT list.
Note that this item need not be a number; it can be any unique
identifier.
diffrn
Data items in the DIFFRN category record details about the
diffraction data and their measurement.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:diffrnCategory>
<PDBx:diffrn id="Set1">
<PDBx:ambient_environment> Mother liquor from the reservoir of the vapor diffusion experiment, mounted in room air</PDBx:ambient_environment>
<PDBx:ambient_temp>293.0</PDBx:ambient_temp>
<PDBx:crystal_support> 0.7 mm glass capillary, sealed with dental wax</PDBx:crystal_support>
<PDBx:crystal_treatment> Equilibrated in rotating anode radiation enclosure for
18 hours prior to beginning of data collection</PDBx:crystal_treatment>
</PDBx:diffrn>
</PDBx:diffrnCategory>
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
<PDBx:diffrnCategory>
<PDBx:diffrn id="d1">
<PDBx:ambient_temp>293</PDBx:ambient_temp>
<PDBx:details> \q scan width (1.0 + 0.14tan\q)\%, \q scan rate 1.2\% per
min. Background counts for 5 sec on each side every scan.</PDBx:details>
</PDBx:diffrn>
</PDBx:diffrnCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
0
1
0
1
0
1
1
diffrnCategory
This property indicates that datablock
has a category element diffrn.
diffrnItem
Abstract Datatype property for diffrn items.
reference_to_diffrn
cross-reference to diffrn
diffrn.ambient_environment
The gas or liquid surrounding the sample, if not air.
diffrn.ambient_pressure
The mean hydrostatic pressure in kilopascals at which the
intensities were measured.
diffrn.ambient_pressure_esd
The estimated standard deviation of attribute ambient_pressure in category diffrn.
diffrn.ambient_pressure_gt
The mean hydrostatic pressure in kilopascals above which
the intensities were measured. attribute ambient_pressure_gt in category diffrn and
attribute ambient_pressure_lt in category diffrn allow a pressure range to be given.
attribute ambient_pressure in category diffrn should always be used in
preference to these two items whenever possible.
diffrn.ambient_pressure_lt
The mean hydrostatic pressure in kilopascals below which
the intensities were measured. attribute ambient_pressure_gt in category diffrn and
attribute ambient_pressure_lt in category diffrn allow a pressure range to be given.
attribute ambient_pressure in category diffrn should always be used in
preference to these two items whenever possible.
diffrn.ambient_temp
The mean temperature in kelvins at which the intensities were
measured.
diffrn.ambient_temp_details
A description of special aspects of temperature control during
data collection.
diffrn.ambient_temp_esd
The standard uncertainty (estimated standard deviation)
of attribute ambient_temp in category diffrn.
diffrn.ambient_temp_gt
The mean temperature in kelvins above which the intensities were
measured. _diffrn.ambient_temp_gt and _diffrn.ambient_temp_lt
allow a range of temperatures to be given.
attribute ambient_temp in category diffrn should always be used in preference
to these two items whenever possible.
diffrn.ambient_temp_lt
The mean temperature in kelvins below which the intensities were
measured. _diffrn.ambient_temp_gt and _diffrn.ambient_temp_lt
allow a range of temperatures to be given.
attribute ambient_temp in category diffrn should always be used in preference
to these two items whenever possible.
diffrn.crystal_id
This data item is a pointer to attribute id in category exptl_crystal in the
EXPTL_CRYSTAL category.
diffrn.crystal_support
The physical device used to support the crystal during data
collection.
glass capillary
quartz capillary
fiber
metal loop
diffrn.crystal_treatment
Remarks about how the crystal was treated prior to intensity
measurement. Particularly relevant when intensities were
measured at low temperature.
equilibrated in hutch for 24 hours
flash frozen in liquid nitrogen
slow cooled with direct air stream
diffrn.details
Special details of the diffraction measurement process. Should
include information about source instability, crystal motion,
degradation and so on.
diffrn.id
This data item uniquely identifies a set of diffraction
data.
diffrn_attenuator
Data items in the DIFFRN_ATTENUATOR category record details
about the diffraction attenuator scales employed.
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<PDBx:diffrn_attenuatorCategory>
<PDBx:diffrn_attenuator code="1">
<PDBx:scale>16.976</PDBx:scale>
</PDBx:diffrn_attenuator>
</PDBx:diffrn_attenuatorCategory>
0
1
0
1
1
diffrn_attenuatorCategory
This property indicates that datablock
has a category element diffrn_attenuator.
diffrn_attenuatorItem
Abstract Datatype property for diffrn_attenuator items.
reference_to_diffrn_attenuator
cross-reference to diffrn_attenuator
diffrn_attenuator.material
Material from which the attenuator is made.
diffrn_attenuator.scale
The scale factor applied when an intensity measurement is
reduced by an attenuator identified by attribute code.
in category diffrn_attenuator The measured intensity must be multiplied by this scale to
convert it to the same scale as unattenuated intensities.
diffrn_attenuator.code
A code associated with a particular attenuator setting. This
code is referenced by the attribute attenuator_code in category diffrn_refln which is
stored with the diffraction data. See attribute scale in category diffrn_attenuator.
diffrn_detector
Data items in the DIFFRN_DETECTOR category describe the
detector used to measure the scattered radiation, including
any analyser and post-sample collimation.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:diffrn_detectorCategory>
<PDBx:diffrn_detector diffrn_id="d1">
<PDBx:detector>multiwire</PDBx:detector>
<PDBx:type>Siemens</PDBx:type>
</PDBx:diffrn_detector>
</PDBx:diffrn_detectorCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
diffrn_detectorCategory
This property indicates that datablock
has a category element diffrn_detector.
diffrn_detectorItem
Abstract Datatype property for diffrn_detector items.
reference_to_diffrn_detector
cross-reference to diffrn_detector
diffrn_detector.area_resol_mean
The resolution of an area detector, in pixels/mm.
diffrn_detector.details
A description of special aspects of the radiation detector.
diffrn_detector.detector
The general class of the radiation detector.
photographic film
scintillation counter
CCD plate
BF~3~ counter
diffrn_detector.dtime
The deadtime in microseconds of the detector used to measure
the diffraction intensities.
diffrn_detector.pdbx_collection_date
The date of data collection.
1996-12-25
diffrn_detector.pdbx_collection_time_total
The total number of seconds required to measure this
data set.
120.0
diffrn_detector.pdbx_frames_total
The total number of data frames collected for this
data set.
20
100
diffrn_detector.type
The make, model or name of the detector device used.
diffrn_detector.diffrn_id
This data item is a pointer to attribute id in category diffrn in the DIFFRN
category.
diffrn_measurement
Data items in the DIFFRN_MEASUREMENT category record details
about the device used to orient and/or position the crystal
during data measurement and the manner in which the diffraction
data were measured.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:diffrn_measurementCategory>
<PDBx:diffrn_measurement diffrn_id="d1">
<PDBx:details> 440 frames, 0.20 degrees, 150 sec, detector distance 12 cm,
detector angle 22.5 degrees</PDBx:details>
<PDBx:device>3-circle camera</PDBx:device>
<PDBx:device_details>none</PDBx:device_details>
<PDBx:device_type>Supper model x</PDBx:device_type>
<PDBx:method>omega scan</PDBx:method>
</PDBx:diffrn_measurement>
</PDBx:diffrn_measurementCategory>
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<PDBx:diffrn_measurementCategory>
<PDBx:diffrn_measurement diffrn_id="s1">
<PDBx:device_type>Philips PW1100/20 diffractometer</PDBx:device_type>
<PDBx:method>\q/2\q</PDBx:method>
</PDBx:diffrn_measurement>
</PDBx:diffrn_measurementCategory>
0
1
0
1
0
1
0
1
0
1
0
1
1
diffrn_measurementCategory
This property indicates that datablock
has a category element diffrn_measurement.
diffrn_measurementItem
Abstract Datatype property for diffrn_measurement items.
reference_to_diffrn_measurement
cross-reference to diffrn_measurement
diffrn_measurement.details
A description of special aspects of the intensity measurement.
440 frames, 0.20 degrees, 150 sec, detector
distance 12 cm, detector angle 22.5 degrees
diffrn_measurement.device
The general class of goniometer or device used to support and
orient the specimen.
3-circle camera
4-circle camera
kappa-geometry camera
oscillation camera
precession camera
diffrn_measurement.device_details
A description of special aspects of the device used to measure
the diffraction intensities.
commercial goniometer modified locally to
allow for 90\% \t arc
diffrn_measurement.device_type
The make, model or name of the measurement device
(goniometer) used.
Supper model q
Huber model r
Enraf-Nonius model s
homemade
diffrn_measurement.method
Method used to measure intensities.
profile data from theta/2theta scans
diffrn_measurement.specimen_support
The physical device used to support the crystal during data
collection.
glass capillary
quartz capillary
fiber
metal loop
diffrn_measurement.diffrn_id
This data item is a pointer to attribute id in category diffrn in the DIFFRN
category.
diffrn_orient_matrix
Data items in the DIFFRN_ORIENT_MATRIX category record details
about the orientation matrix used in the measurement of the
diffraction data.
Example 1 - based on CAD-4 diffractometer data obtained for
Yb(S-C5H4N)2(THF)4.
<PDBx:diffrn_orient_matrixCategory>
<PDBx:diffrn_orient_matrix diffrn_id="set1">
<PDBx:UB11>-0.071479</PDBx:UB11>
<PDBx:UB12>0.020208</PDBx:UB12>
<PDBx:UB13>0.039076</PDBx:UB13>
<PDBx:UB21>0.035372</PDBx:UB21>
<PDBx:UB22>0.056209</PDBx:UB22>
<PDBx:UB23>0.078324</PDBx:UB23>
<PDBx:UB31>-0.007470</PDBx:UB31>
<PDBx:UB32>0.067854</PDBx:UB32>
<PDBx:UB33>-0.017832</PDBx:UB33>
<PDBx:type> reciprocal axis matrix, multiplies hkl vector to generate
diffractometer xyz vector and diffractometer angles</PDBx:type>
</PDBx:diffrn_orient_matrix>
</PDBx:diffrn_orient_matrixCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
diffrn_orient_matrixCategory
This property indicates that datablock
has a category element diffrn_orient_matrix.
diffrn_orient_matrixItem
Abstract Datatype property for diffrn_orient_matrix items.
reference_to_diffrn_orient_matrix
cross-reference to diffrn_orient_matrix
diffrn_orient_matrix.UB11
The [1][1] element of the 3x3 matrix that defines the dimensions
of the reciprocal cell and its orientation with respect to the
local diffractometer axes. See also attribute type in category diffrn_orient_matrix.
diffrn_orient_matrix.UB12
The [1][2] element of the 3x3 matrix that defines the dimensions
of the reciprocal cell and its orientation with respect to the
local diffractometer axes. See also attribute type in category diffrn_orient_matrix.
diffrn_orient_matrix.UB13
The [1][3] element of the 3x3 matrix that defines the dimensions
of the reciprocal cell and its orientation with respect to the
local diffractometer axes. See also attribute type in category diffrn_orient_matrix.
diffrn_orient_matrix.UB21
The [2][1] element of the 3x3 matrix that defines the dimensions
of the reciprocal cell and its orientation with respect to the
local diffractometer axes. See also attribute type in category diffrn_orient_matrix.
diffrn_orient_matrix.UB22
The [2][2] element of the 3x3 matrix that defines the dimensions
of the reciprocal cell and its orientation with respect to the
local diffractometer axes. See also attribute type in category diffrn_orient_matrix.
diffrn_orient_matrix.UB23
The [2][3] element of the 3x3 matrix that defines the dimensions
of the reciprocal cell and its orientation with respect to the
local diffractometer axes. See also attribute type in category diffrn_orient_matrix.
diffrn_orient_matrix.UB31
The [3][1] element of the 3x3 matrix that defines the dimensions
of the reciprocal cell and its orientation with respect to the
local diffractometer axes. See also attribute type in category diffrn_orient_matrix.
diffrn_orient_matrix.UB32
The [3][2] element of the 3x3 matrix that defines the dimensions
of the reciprocal cell and its orientation with respect to the
local diffractometer axes. See also attribute type in category diffrn_orient_matrix.
diffrn_orient_matrix.UB33
The [3][3] element of the 3x3 matrix that defines the dimensions
of the reciprocal cell and its orientation with respect to the
local diffractometer axes. See also attribute type in category diffrn_orient_matrix.
diffrn_orient_matrix.type
A description of the orientation matrix type and how it should
be applied to define the orientation of the crystal precisely
with respect to the diffractometer axes.
diffrn_orient_matrix.diffrn_id
This data item is a pointer to attribute id in category diffrn in the DIFFRN
category.
diffrn_orient_refln
Data items in the DIFFRN_ORIENT_REFLN category record details
about the reflections that define the orientation matrix used in
the measurement of the diffraction intensities.
Example 1 - based on CAD-4 diffractometer data obtained for
Yb(S-C5H4N)2(THF)4.
<PDBx:diffrn_orient_reflnCategory>
<PDBx:diffrn_orient_refln diffrn_id="myset1" index_h="2" index_k="0" index_l="2">
<PDBx:angle_chi>-28.45</PDBx:angle_chi>
<PDBx:angle_kappa>-11.32</PDBx:angle_kappa>
<PDBx:angle_omega>5.33</PDBx:angle_omega>
<PDBx:angle_phi>101.78</PDBx:angle_phi>
<PDBx:angle_psi>0.00</PDBx:angle_psi>
<PDBx:angle_theta>10.66</PDBx:angle_theta>
</PDBx:diffrn_orient_refln>
</PDBx:diffrn_orient_reflnCategory>
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
diffrn_orient_reflnCategory
This property indicates that datablock
has a category element diffrn_orient_refln.
diffrn_orient_reflnItem
Abstract Datatype property for diffrn_orient_refln items.
reference_to_diffrn_orient_refln
cross-reference to diffrn_orient_refln
diffrn_orient_refln.angle_chi
Diffractometer angle chi of a reflection used to
define the orientation matrix in degrees. See
attribute UB[][] in category diffrn_orient_matrix and the Miller indices
in the DIFFRN_ORIENT_REFLN category.
diffrn_orient_refln.angle_kappa
Diffractometer angle kappa of a reflection used to
define the orientation matrix in degrees. See
attribute UB[][] in category diffrn_orient_matrix and the Miller indices
in the DIFFRN_ORIENT_REFLN category.
diffrn_orient_refln.angle_omega
Diffractometer angle omega of a reflection used to
define the orientation matrix in degrees. See
attribute UB[][] in category diffrn_orient_matrix and the Miller indices in
the DIFFRN_ORIENT_REFLN category.
diffrn_orient_refln.angle_phi
Diffractometer angle phi of a reflection used to
define the orientation matrix in degrees. See
attribute UB[][] in category diffrn_orient_matrix and the Miller indices
in the DIFFRN_ORIENT_REFLN category.
diffrn_orient_refln.angle_psi
Diffractometer angle psi of a reflection used to
define the orientation matrix in degrees. See
attribute UB[][] in category diffrn_orient_matrix and the Miller indices
in the DIFFRN_ORIENT_REFLN category.
diffrn_orient_refln.angle_theta
Diffractometer angle theta of a reflection used to
define the orientation matrix in degrees. See
attribute UB[][] in category diffrn_orient_matrix and the Miller indices
in the DIFFRN_ORIENT_REFLN category.
diffrn_orient_refln.diffrn_id
This data item is a pointer to attribute id in category diffrn in the DIFFRN
category.
diffrn_orient_refln.index_h
Miller index h of a reflection used to define the orientation
matrix.
diffrn_orient_refln.index_k
Miller index k of a reflection used to define the orientation
matrix.
diffrn_orient_refln.index_l
Miller index l of a reflection used to define the orientation
matrix.
diffrn_radiation
Data items in the DIFFRN_RADIATION category describe
the radiation used in measuring the diffraction intensities,
its collimation and monochromatization before the sample.
Post-sample treatment of the beam is described by data
items in the DIFFRN_DETECTOR category.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:diffrn_radiationCategory>
<PDBx:diffrn_radiation diffrn_id="set1">
<PDBx:collimation>0.3 mm double pinhole</PDBx:collimation>
<PDBx:monochromator>graphite</PDBx:monochromator>
<PDBx:type>Cu K\a</PDBx:type>
<PDBx:wavelength_id>1</PDBx:wavelength_id>
</PDBx:diffrn_radiation>
</PDBx:diffrn_radiationCategory>
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<PDBx:diffrn_radiationCategory>
<PDBx:diffrn_radiation diffrn_id="set1">
<PDBx:monochromator>graphite</PDBx:monochromator>
<PDBx:type>Cu K\a</PDBx:type>
<PDBx:wavelength_id>1</PDBx:wavelength_id>
</PDBx:diffrn_radiation>
</PDBx:diffrn_radiationCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
0
1
1
diffrn_radiationCategory
This property indicates that datablock
has a category element diffrn_radiation.
diffrn_radiationItem
Abstract Datatype property for diffrn_radiation items.
reference_to_diffrn_radiation
cross-reference to diffrn_radiation
diffrn_radiation.collimation
The collimation or focusing applied to the radiation.
0.3 mm double-pinhole
0.5 mm
focusing mirrors
diffrn_radiation.filter_edge
Absorption edge in angstroms of the radiation filter used.
diffrn_radiation.inhomogeneity
Half-width in millimetres of the incident beam in the
direction perpendicular to the diffraction plane.
diffrn_radiation.monochromator
The method used to obtain monochromatic radiation. If a mono-
chromator crystal is used, the material and the indices of the
Bragg reflection are specified.
Zr filter
Ge 220
none
equatorial mounted graphite
diffrn_radiation.pdbx_analyzer
Indicates the method used to obtain monochromatic radiation.
attribute monochromator in category diffrn_radiation describes the primary beam
monochromator (pre-specimen monochromation).
attribute pdbx_analyzer in category diffrn_radiation specifies the
post-diffraction analyser (post-specimen) monochromation.
Note that monochromators may have either 'parallel' or
'antiparallel' orientation. It is assumed that the
geometry is parallel unless specified otherwise.
In a parallel geometry, the position of the monochromator
allows the incident beam and the final post-specimen
and post-monochromator beam to be as close to parallel
as possible. In a parallel geometry, the diffracting
planes in the specimen and monochromator will be parallel
when 2*theta(monochromator) is equal to 2*theta (specimen).
For further discussion see R. Jenkins and R. Snyder,
Introduction to X-ray Powder Diffraction, Wiley (1996),
pp. 164-5.
GE(111)
Zr filter
Ge 220
none
equatorial mounted graphite (0001)
Si (111), antiparallel
diffrn_radiation.pdbx_diffrn_protocol
SINGLE WAVELENGTH, LAUE, or MAD.
SINGLE WAVELENGTH
MONOCHROMATIC
LAUE
MAD
OTHER
M
L
Monochromatic or Laue.
M
L
diffrn_radiation.pdbx_wavelength
Wavelength of radiation.
diffrn_radiation.pdbx_wavelength_list
Comma separated list of wavelengths or wavelength range.
diffrn_radiation.polarisn_norm
The angle in degrees, as viewed from the specimen, between the
perpendicular component of the polarization and the diffraction
plane. See attribute polarisn_ratio in category diffrn_radiation.
diffrn_radiation.polarisn_ratio
Polarization ratio of the diffraction beam incident on the
crystal. This is the ratio of the perpendicularly polarized
to the parallel-polarized component of the radiation. The
perpendicular component forms an angle of
attribute polarisn_norm in category diffrn_radiation to the normal to the
diffraction plane of the sample (i.e. the plane containing
the incident and reflected beams).
x-ray
neutron
electron
gamma
The nature of the radiation used (i.e. the name of the
subatomic particle or the region of the electromagnetic
spectrum). It is strongly recommended that this information
is given, so that the probe radiation can be simply determined.
diffrn_radiation.type
The nature of the radiation. This is typically a description
of the X-ray wavelength in Siegbahn notation.
CuK\a
Cu K\a~1~
Cu K-L~2,3~
white-beam
diffrn_radiation.wavelength_id
This data item is a pointer to attribute id
in category diffrn_radiation_wavelength in the DIFFRN_RADIATION_WAVELENGTH category.
K-L~3~
K-L~2~
K-M~3~
K-L~2,3~
The IUPAC symbol for the X-ray wavelength for the probe
radiation.
diffrn_radiation.diffrn_id
This data item is a pointer to attribute id in category diffrn in the DIFFRN
category.
diffrn_radiation_wavelength
Data items in the DIFFRN_RADIATION_WAVELENGTH category
describe the wavelength of the radiation used to measure the
diffraction intensities. Items may be looped to identify
and assign weights to distinct components of a
polychromatic beam.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:diffrn_radiation_wavelengthCategory>
<PDBx:diffrn_radiation_wavelength id="1">
<PDBx:wavelength>1.54</PDBx:wavelength>
<PDBx:wt>1.0</PDBx:wt>
</PDBx:diffrn_radiation_wavelength>
</PDBx:diffrn_radiation_wavelengthCategory>
1
1
0
1
1
diffrn_radiation_wavelengthCategory
This property indicates that datablock
has a category element diffrn_radiation_wavelength.
diffrn_radiation_wavelengthItem
Abstract Datatype property for diffrn_radiation_wavelength items.
reference_to_diffrn_radiation_wavelength
cross-reference to diffrn_radiation_wavelength
diffrn_radiation_wavelength.wavelength
The radiation wavelength in angstroms.
diffrn_radiation_wavelength.wt
The relative weight of a wavelength identified by the code
attribute id in category diffrn_radiation_wavelength in the list of wavelengths.
diffrn_radiation_wavelength.id
The code identifying each value of
attribute wavelength.
in category diffrn_radiation_wavelength Items in the DIFFRN_RADIATION_WAVELENGTH category are looped
when multiple wavelengths are used.
This code is used to link with the DIFFRN_REFLN category.
The attribute wavelength_id in category diffrn_refln codes must match one of
the codes defined in this category.
x1
x2
neut
diffrn_refln
Data items in the DIFFRN_REFLN category record details about
the intensities in the diffraction data set
identified by attribute diffrn_id.
in category diffrn_refln
The DIFFRN_REFLN data items refer to individual intensity
measurements and must be included in looped lists.
The DIFFRN_REFLNS data items specify the parameters that apply
to all intensity measurements in the particular diffraction
data set identified by attribute diffrn_id in category diffrn_reflns.
Example 1 - based on CAD-4 diffractometer data obtained for
Yb(S-C5H4N)2(THF)4 for data set 'set1' reflection 1102.
<PDBx:diffrn_reflnCategory>
<PDBx:diffrn_refln diffrn_id="set1" id="1102">
<PDBx:angle_chi>32.21</PDBx:angle_chi>
<PDBx:angle_kappa>20.12</PDBx:angle_kappa>
<PDBx:angle_omega>11.54</PDBx:angle_omega>
<PDBx:angle_phi>176.02</PDBx:angle_phi>
<PDBx:angle_psi>0.00</PDBx:angle_psi>
<PDBx:angle_theta>23.08</PDBx:angle_theta>
<PDBx:attenuator_code>Ni.005</PDBx:attenuator_code>
<PDBx:counts_bg_1>22</PDBx:counts_bg_1>
<PDBx:counts_bg_2>25</PDBx:counts_bg_2>
<PDBx:counts_net>3450</PDBx:counts_net>
<PDBx:counts_peak>321</PDBx:counts_peak>
<PDBx:counts_total>3499</PDBx:counts_total>
<PDBx:detect_slit_horiz>0.04</PDBx:detect_slit_horiz>
<PDBx:detect_slit_vert>0.02</PDBx:detect_slit_vert>
<PDBx:elapsed_time>1.00</PDBx:elapsed_time>
<PDBx:index_h>4</PDBx:index_h>
<PDBx:index_k>0</PDBx:index_k>
<PDBx:index_l>2</PDBx:index_l>
<PDBx:intensity_net>202.56</PDBx:intensity_net>
<PDBx:intensity_sigma>2.18</PDBx:intensity_sigma>
<PDBx:scale_group_code>A24</PDBx:scale_group_code>
<PDBx:scan_mode>om</PDBx:scan_mode>
<PDBx:scan_mode_backgd>mo</PDBx:scan_mode_backgd>
<PDBx:scan_rate>1.2</PDBx:scan_rate>
<PDBx:scan_time_backgd>900.00</PDBx:scan_time_backgd>
<PDBx:scan_width>1.0</PDBx:scan_width>
<PDBx:sint_over_lambda>0.25426</PDBx:sint_over_lambda>
<PDBx:standard_code>1</PDBx:standard_code>
<PDBx:wavelength>1.54184</PDBx:wavelength>
<PDBx:wavelength_id>Cu1fixed</PDBx:wavelength_id>
</PDBx:diffrn_refln>
</PDBx:diffrn_reflnCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
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1
diffrn_reflnCategory
This property indicates that datablock
has a category element diffrn_refln.
diffrn_reflnItem
Abstract Datatype property for diffrn_refln items.
reference_to_diffrn_refln
cross-reference to diffrn_refln
diffrn_refln.angle_chi
The diffractometer angle chi of a reflection in degrees. This
angle corresponds to the specified orientation matrix
and the original measured cell before any subsequent cell
transformations.
diffrn_refln.angle_kappa
The diffractometer angle kappa of a reflection in degrees. This
angle corresponds to the specified orientation matrix
and the original measured cell before any subsequent cell
transformations.
diffrn_refln.angle_omega
The diffractometer angle omega of a reflection in degrees. This
angle corresponds to the specified orientation matrix
and the original measured cell before any subsequent cell
transformations.
diffrn_refln.angle_phi
The diffractometer angle phi of a reflection in degrees. This
angle corresponds to the specified orientation matrix
and the original measured cell before any subsequent cell
transformations.
diffrn_refln.angle_psi
The diffractometer angle psi of a reflection in degrees. This
angle corresponds to the specified orientation matrix
and the original measured cell before any subsequent cell
transformations.
diffrn_refln.angle_theta
The diffractometer angle theta of a reflection in degrees. This
angle corresponds to the specified orientation matrix
and the original measured cell before any subsequent cell
transformations.
diffrn_refln.attenuator_code
The code identifying the attenuator setting for this reflection.
This code must match one of the attribute code in category diffrn_attenuator values.
diffrn_refln.class_code
The code identifying the class to which this reflection has
been assigned. This code must match a value of
attribute code in category diffrn_reflns_class. Reflections may be grouped into
classes for a variety of purposes. For example, for modulated
structures each reflection class may be defined by the
number m=sum|m~i~|, where the m~i~ are the integer coefficients
that, in addition to h,k,l, index the corresponding diffraction
vector in the basis defined for the reciprocal lattice.
diffrn_refln.counts_bg_1
The diffractometer counts for the measurement of the background
before the peak.
diffrn_refln.counts_bg_2
The diffractometer counts for the measurement of the background
after the peak.
diffrn_refln.counts_net
The diffractometer counts for the measurement of net counts after
background removal.
diffrn_refln.counts_peak
The diffractometer counts for the measurement of counts for the
peak scan or position.
diffrn_refln.counts_total
The diffractometer counts for the measurement of total counts
(background plus peak).
diffrn_refln.detect_slit_horiz
Total slit aperture in degrees in the diffraction plane.
diffrn_refln.detect_slit_vert
Total slit aperture in degrees perpendicular to the
diffraction plane.
diffrn_refln.elapsed_time
Elapsed time in minutes from the start of the diffraction
experiment to the measurement of this intensity.
diffrn_refln.index_h
Miller index h of a reflection. The values of
the Miller indices in the DIFFRN_REFLN category need not match
the values of the Miller indices in the REFLN category if a
transformation of the original measured cell has taken place.
Details of the cell transformation are given in
attribute reduction_process in category diffrn_reflns. See also
attribute transf_matrix[][] in category diffrn_reflns.
diffrn_refln.index_k
Miller index k of a reflection. The values of
the Miller indices in the DIFFRN_REFLN category need not match
the values of the Miller indices in the REFLN category if a
transformation of the original measured cell has taken place.
Details of the cell transformation are given in
attribute reduction_process in category diffrn_reflns. See also
attribute transf_matrix[][] in category diffrn_reflns.
diffrn_refln.index_l
Miller index l of a reflection. The values of
the Miller indices in the DIFFRN_REFLN category need not match
the values of the Miller indices in the REFLN category if a
transformation of the original measured cell has taken place.
Details of the cell transformation are given in
attribute reduction_process in category diffrn_reflns. See also
attribute transf_matrix[][] in category diffrn_reflns.
diffrn_refln.intensity_net
Net intensity calculated from the diffraction counts after the
attenuator and standard scales have been applied.
diffrn_refln.intensity_sigma
Standard uncertainty (estimated standard deviation) of the
intensity calculated from the diffraction counts after the
attenuator and standard scales have been applied.
diffrn_refln.intensity_u
Standard uncertainty of the net intensity calculated from
the diffraction counts after the attenuator and standard
scales have been applied.
diffrn_refln.scale_group_code
The code identifying the scale applying to this reflection.
This data item is a pointer to attribute code in category diffrn_scale_group in the
DIFFRN_SCALE_GROUP category.
om
ot
q
The code identifying the mode of scanning for measurements
using a diffractometer.
See _diffrn_refln.scan_width and _diffrn_refln.scan_mode_backgd.
st
mo
The code identifying the mode of scanning a reflection to
measure the background intensity.
diffrn_refln.scan_rate
The rate of scanning a reflection in degrees per minute
to measure the intensity.
diffrn_refln.scan_time_backgd
The time spent measuring each background in seconds.
diffrn_refln.scan_width
The scan width in degrees of the scan mode defined by the code
attribute scan_mode in category diffrn_refln.
diffrn_refln.sint_over_lambda
The (sin theta)/lambda value in reciprocal angstroms for this
reflection.
diffrn_refln.standard_code
The code identifying that this reflection was measured as a
standard intensity.
This data item is a pointer to attribute code in category diffrn_standard_refln in the
DIFFRN_STANDARD_REFLN category.
diffrn_refln.wavelength
The mean wavelength in angstroms of the radiation used to measure
the intensity of this reflection. This is an important parameter
for data collected using energy-dispersive detectors or the
Laue method.
diffrn_refln.wavelength_id
This data item is a pointer to attribute wavelength_id in category diffrn_radiation in
the DIFFRN_RADIATION category.
diffrn_refln.diffrn_id
This data item is a pointer to attribute id in category diffrn in the DIFFRN
category.
diffrn_refln.id
The value of attribute id in category diffrn_refln must uniquely identify the
reflection in the data set identified by the item
attribute diffrn_id.
in category diffrn_refln
Note that this item need not be a number; it can be any unique
identifier.
diffrn_reflns
Data items in the DIFFRN_REFLNS category record details about
the set of intensities measured in the diffraction experiment.
The DIFFRN_REFLN data items refer to individual intensity
measurements and must be included in looped lists.
The DIFFRN_REFLNS data items specify the parameters that apply
to all intensity measurements in a diffraction data set.
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
diffrn_reflnsCategory
This property indicates that datablock
has a category element diffrn_reflns.
diffrn_reflnsItem
Abstract Datatype property for diffrn_reflns items.
reference_to_diffrn_reflns
cross-reference to diffrn_reflns
diffrn_reflns.av_R_equivalents
The residual [sum|avdel(I)| / sum|av(I)|] for symmetry-equivalent
reflections used to calculate the average intensity av(I). The
avdel(I) term is the average absolute difference between av(I)
and the individual symmetry-equivalent intensities.
diffrn_reflns.av_sigmaI_over_netI
Measure [sum|sigma(I)|/sum|net(I)|] for all measured reflections.
diffrn_reflns.av_unetI_over_netI
Measure [sum u(net I)|/sum|net I|] for all measured reflections.
diffrn_reflns.limit_h_max
The maximum value of the Miller index h for the
reflection data specified by attribute index_h in category diffrn_refln.
diffrn_reflns.limit_h_min
The minimum value of the Miller index h for the
reflection data specified by attribute index_h in category diffrn_refln.
diffrn_reflns.limit_k_max
The maximum value of the Miller index k for the
reflection data specified by attribute index_k in category diffrn_refln.
diffrn_reflns.limit_k_min
The minimum value of the Miller index k for the
reflection data specified by attribute index_k in category diffrn_refln.
diffrn_reflns.limit_l_max
The maximum value of the Miller index l for the
reflection data specified by attribute index_l in category diffrn_refln.
diffrn_reflns.limit_l_min
The minimum value of the Miller index l for the
reflection data specified by attribute index_l in category diffrn_refln.
diffrn_reflns.number
The total number of measured intensities, excluding reflections
that are classified as systematically absent.
diffrn_reflns.pdbx_Rmerge_I_obs
The R factor for merging the reflections that satisfy the
resolution limits established by attribute d_resolution_high
in category diffrn_reflns and attribute d_resolution_low in category diffrn_reflns and the observation limit
established by attribute observed_criterion.
in category diffrn_reflns
Rmerge(I) = [sum~i~(sum~j~|I~j~ - |)] / [sum~i~(sum~j~)]
I~j~ = the intensity of the jth observation of reflection i
= the mean of the amplitudes of all observations of
reflection i
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection
diffrn_reflns.pdbx_Rsym_value
The R factor for averaging the symmetry related reflections to a
unique data set.
diffrn_reflns.pdbx_chi_squared
Overall Chi-squared statistic for the data set.
diffrn_reflns.pdbx_d_res_high
The highest resolution for the interplanar spacings in the
reflection data set. This is the smallest d value.
diffrn_reflns.pdbx_d_res_low
The lowest resolution for the interplanar spacings in the
reflection data set. This is the largest d value.
diffrn_reflns.pdbx_number_obs
The number of reflections satisfying the observation criterion
as in attribute pdbx_observed_criterion
in category diffrn_reflns
diffrn_reflns.pdbx_observed_criterion
The criterion used to classify a reflection as 'observed'. This
criterion is usually expressed in terms of a sigma(I) or
sigma(F) threshold.
diffrn_reflns.pdbx_percent_possible_obs
The percentage of geometrically possible reflections represented
by reflections that satisfy the resolution limits established
by _diffrn_reflns.d_resolution_high and _diffrn_reflns.d_resolution_low and
the observation limit established by attribute observed_criterion.
in category diffrn_reflns
diffrn_reflns.pdbx_redundancy
The overall redundancy for the data set.
diffrn_reflns.pdbx_rejects
The number of rejected reflections in the data set.
The reflections may be rejected by setting the
observation criterion, attribute observed_criterion in category diffrn_reflns.
diffrn_reflns.reduction_process
A description of the process used to reduce the intensity data
into structure-factor magnitudes.
data averaged using Fisher test
diffrn_reflns.theta_max
Maximum theta angle in degrees for the measured diffraction
intensities.
diffrn_reflns.theta_min
Minimum theta angle in degrees for the measured diffraction
intensities.
diffrn_reflns.transf_matrix11
The [1][1] element of the 3x3 matrix used to transform Miller
indices in the DIFFRN_REFLN category into the Miller indices in
the REFLN category.
diffrn_reflns.transf_matrix12
The [1][2] element of the 3x3 matrix used to transform Miller
indices in the DIFFRN_REFLN category into the Miller indices in
the REFLN category.
diffrn_reflns.transf_matrix13
The [1][3] element of the 3x3 matrix used to transform Miller
indices in the DIFFRN_REFLN category into the Miller indices in
the REFLN category.
diffrn_reflns.transf_matrix21
The [2][1] element of the 3x3 matrix used to transform Miller
indices in the DIFFRN_REFLN category into the Miller indices in
the REFLN category.
diffrn_reflns.transf_matrix22
The [2][2] element of the 3x3 matrix used to transform Miller
indices in the DIFFRN_REFLN category into the Miller indices in
the REFLN category.
diffrn_reflns.transf_matrix23
The [2][3] element of the 3x3 matrix used to transform Miller
indices in the DIFFRN_REFLN category into the Miller indices in
the REFLN category.
diffrn_reflns.transf_matrix31
The [3][1] element of the 3x3 matrix used to transform Miller
indices in the DIFFRN_REFLN category into the Miller indices in
the REFLN category.
diffrn_reflns.transf_matrix32
The [3][2] element of the 3x3 matrix used to transform Miller
indices in the DIFFRN_REFLN category into the Miller indices in
the REFLN category.
diffrn_reflns.transf_matrix33
The [3][3] element of the 3x3 matrix used to transform Miller
indices in the DIFFRN_REFLN category into the Miller indices in
the REFLN category.
diffrn_reflns.diffrn_id
This data item is a pointer to attribute id in category diffrn in the DIFFRN
category.
diffrn_reflns_class
Data items in the DIFFRN_REFLNS_CLASS category record details
about the classes of reflections measured in the diffraction
experiment.
Example 1 - example corresponding to the one-dimensional incommensurately
modulated structure of K~2~SeO~4~. Each reflection class is
defined by the number m=sum|m~i~|, where the m~i~ are the
integer coefficients that, in addition to h,k,l, index the
corresponding diffraction vector in the basis defined for
the reciprocal lattice.
<PDBx:diffrn_reflns_classCategory>
<PDBx:diffrn_reflns_class code="Main">
<PDBx:av_R_eq>0.015</PDBx:av_R_eq>
<PDBx:d_res_high>0.551</PDBx:d_res_high>
<PDBx:d_res_low>6.136</PDBx:d_res_low>
<PDBx:description>m=0; main reflections</PDBx:description>
<PDBx:number>1580</PDBx:number>
</PDBx:diffrn_reflns_class>
<PDBx:diffrn_reflns_class code="Sat1">
<PDBx:av_R_eq>0.010</PDBx:av_R_eq>
<PDBx:d_res_high>0.551</PDBx:d_res_high>
<PDBx:d_res_low>6.136</PDBx:d_res_low>
<PDBx:description>m=1; first-order satellites</PDBx:description>
<PDBx:number>1045</PDBx:number>
</PDBx:diffrn_reflns_class>
</PDBx:diffrn_reflns_classCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
diffrn_reflns_classCategory
This property indicates that datablock
has a category element diffrn_reflns_class.
diffrn_reflns_classItem
Abstract Datatype property for diffrn_reflns_class items.
reference_to_diffrn_reflns_class
cross-reference to diffrn_reflns_class
diffrn_reflns_class.av_R_eq
For each reflection class, the residual
[sum av|del(I)|/sum|av(I)|] for symmetry-equivalent reflections
used to calculate the average intensity av(I). The av|del(I)|
term is the average absolute difference between av(I) and the
individual intensities.
diffrn_reflns_class.av_sgI_over_I
Measure [sum|sigma(net I)|/sum|net I|] for all measured intensities
in a reflection class.
diffrn_reflns_class.av_uI_over_I
Measure [sum|u(net I)|/sum|net I|] for all measured intensities
in a reflection class.
diffrn_reflns_class.d_res_high
The smallest value in angstroms for the interplanar
spacings for the reflections in each measured reflection class.
This is called the highest resolution for this reflection class.
diffrn_reflns_class.d_res_low
The largest value in angstroms of the interplanar
spacings for the reflections for each measured reflection class.
This is called the lowest resolution for this reflection class.
diffrn_reflns_class.description
Description of each reflection class.
m=1 first order satellites
H0L0 common projection reflections
diffrn_reflns_class.number
The total number of measured intensities for each reflection
class, excluding the systematic absences arising from
centring translations.
diffrn_reflns_class.code
The code identifying a certain reflection class.
1
m1
s2
diffrn_scale_group
Data items in the DIFFRN_SCALE_GROUP category record details
of the scaling factors applied to place all intensities in the
reflection lists on a common scale.
Scaling groups might, for example, correspond to each film in a
multi-film data set or each crystal in a multi-crystal data set.
Example 1 - based on CAD-4 diffractometer data obtained for
Yb(S-C5H4N)2(THF)4.
<PDBx:diffrn_scale_groupCategory>
<PDBx:diffrn_scale_group code="A24">
<PDBx:I_net>1.021</PDBx:I_net>
</PDBx:diffrn_scale_group>
</PDBx:diffrn_scale_groupCategory>
0
1
1
diffrn_scale_groupCategory
This property indicates that datablock
has a category element diffrn_scale_group.
diffrn_scale_groupItem
Abstract Datatype property for diffrn_scale_group items.
reference_to_diffrn_scale_group
cross-reference to diffrn_scale_group
diffrn_scale_group.I_net
The scale for a specific measurement group which is to be
multiplied with the net intensity to place all intensities
in the DIFFRN_REFLN or REFLN list on a common scale.
diffrn_scale_group.code
The value of attribute code in category diffrn_scale_group must uniquely identify a
record in the DIFFRN_SCALE_GROUP list.
Note that this item need not be a number; it can be any unique
identifier.
1
2
c1
c2
diffrn_source
Data items in the DIFFRN_SOURCE category record details of
the source of radiation used in the diffraction experiment.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:diffrn_sourceCategory>
<PDBx:diffrn_source diffrn_id="s1">
<PDBx:current>180</PDBx:current>
<PDBx:power>50</PDBx:power>
<PDBx:size>8mm x 0.4 mm broad-focus</PDBx:size>
<PDBx:source>rotating anode</PDBx:source>
<PDBx:type>Rigaku RU-200</PDBx:type>
</PDBx:diffrn_source>
</PDBx:diffrn_sourceCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
diffrn_sourceCategory
This property indicates that datablock
has a category element diffrn_source.
diffrn_sourceItem
Abstract Datatype property for diffrn_source items.
reference_to_diffrn_source
cross-reference to diffrn_source
diffrn_source.current
The current in milliamperes at which the radiation source
was operated.
diffrn_source.details
A description of special aspects of the radiation source used.
diffrn_source.pdbx_synchrotron_beamline
Synchrotron beamline.
diffrn_source.pdbx_synchrotron_site
Synchrotron site.
diffrn_source.pdbx_wavelength
Wavelength of radiation.
diffrn_source.pdbx_wavelength_list
Comma separated list of wavelengths or wavelength range.
diffrn_source.power
The power in kilowatts at which the radiation source
was operated.
diffrn_source.size
The dimensions of the source as viewed from the sample.
8mm x 0.4 mm fine-focus
broad focus
diffrn_source.source
The general class of the radiation source.
sealed X-ray tube
nuclear reactor
spallation source
electron microscope
rotating-anode X-ray tube
synchrotron
diffrn_source.take-off_angle
The complement of the angle in degrees between the normal
to the surface of the X-ray tube target and the primary
X-ray beam for beams generated by traditional X-ray tubes.
1.5
H
He
Li
Be
B
C
N
O
F
Ne
Na
Mg
Al
Si
P
S
Cl
Ar
K
Ca
Sc
Ti
V
Cr
Mn
Fe
Co
Ni
Cu
Zn
Ga
Ge
As
Se
Br
Kr
Rb
Sr
Y
Zr
Nb
Mo
Tc
Ru
Rh
Pd
Ag
Cd
In
Sn
Sb
Te
I
Xe
Cs
Ba
La
Ce
Pr
Nd
Pm
Sm
Eu
Gd
Tb
Dy
Ho
Er
Tm
Yb
Lu
Hf
Ta
W
Re
Os
Ir
Pt
Au
Hg
Tl
Pb
Bi
Po
At
Rn
Fr
Ra
Ac
Th
Pa
U
Np
Pu
Am
Cm
Bk
Cf
Es
Fm
Md
No
Lr
The chemical element symbol for the X-ray target
(usually the anode) used to generate X-rays.
This can also be used for spallation sources.
diffrn_source.type
The make, model or name of the source of radiation.
NSLS beamline X8C
Rigaku RU200
diffrn_source.voltage
The voltage in kilovolts at which the radiation source was
operated.
diffrn_source.diffrn_id
This data item is a pointer to attribute id in category diffrn in the DIFFRN
category.
diffrn_standard_refln
Data items in the DIFFRN_STANDARD_REFLN category record details
about the reflections treated as standards during the measurement
of a set of diffraction intensities.
Note that these are the individual standard reflections, not the
results of the analysis of the standard reflections.
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<PDBx:diffrn_standard_reflnCategory>
<PDBx:diffrn_standard_refln code="1" diffrn_id="s1">
<PDBx:index_h>3</PDBx:index_h>
<PDBx:index_k>2</PDBx:index_k>
<PDBx:index_l>4</PDBx:index_l>
</PDBx:diffrn_standard_refln>
<PDBx:diffrn_standard_refln code="1" diffrn_id="s1">
<PDBx:index_h>1</PDBx:index_h>
<PDBx:index_k>9</PDBx:index_k>
<PDBx:index_l>1</PDBx:index_l>
</PDBx:diffrn_standard_refln>
<PDBx:diffrn_standard_refln code="1" diffrn_id="s1">
<PDBx:index_h>3</PDBx:index_h>
<PDBx:index_k>0</PDBx:index_k>
<PDBx:index_l>10</PDBx:index_l>
</PDBx:diffrn_standard_refln>
</PDBx:diffrn_standard_reflnCategory>
1
1
1
1
1
1
1
1
diffrn_standard_reflnCategory
This property indicates that datablock
has a category element diffrn_standard_refln.
diffrn_standard_reflnItem
Abstract Datatype property for diffrn_standard_refln items.
reference_to_diffrn_standard_refln
cross-reference to diffrn_standard_refln
diffrn_standard_refln.index_h
Miller index h of a standard reflection used in the diffraction
measurement process.
diffrn_standard_refln.index_k
Miller index k of a standard reflection used in the diffraction
measurement process.
diffrn_standard_refln.index_l
Miller index l of a standard reflection used in the diffraction
measurement process.
diffrn_standard_refln.code
The code identifying a reflection measured as a standard
reflection with the indices attribute index_h,
in category diffrn_standard_refln attribute index_k in category diffrn_standard_refln and
attribute index_l in category diffrn_standard_refln. This is the same code as the
attribute standard_code in category diffrn_refln in the DIFFRN_REFLN list.
1
2
c1
c2
diffrn_standard_refln.diffrn_id
This data item is a pointer to attribute id in category diffrn in the DIFFRN
category.
diffrn_standards
Data items in the DIFFRN_STANDARDS category record details
about the set of standard reflections used to monitor intensity
stability during the measurement of diffraction intensities.
Note that these records describe properties common to the set of
standard reflections, not the standard reflections themselves.
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<PDBx:diffrn_standardsCategory>
<PDBx:diffrn_standards diffrn_id="s1">
<PDBx:decay_>0</PDBx:decay_>
<PDBx:interval_time>120</PDBx:interval_time>
<PDBx:number>3</PDBx:number>
</PDBx:diffrn_standards>
</PDBx:diffrn_standardsCategory>
0
1
0
1
0
1
0
1
0
1
0
1
1
diffrn_standardsCategory
This property indicates that datablock
has a category element diffrn_standards.
diffrn_standardsItem
Abstract Datatype property for diffrn_standards items.
reference_to_diffrn_standards
cross-reference to diffrn_standards
diffrn_standards.decay_
The percentage decrease in the mean of the intensities
for the set of standard reflections from the start of the
measurement process to the end. This value usually
affords a measure of the overall decay in crystal quality
during the diffraction measurement process. Negative values
are used in exceptional instances where the final intensities
are greater than the initial ones.
diffrn_standards.interval_count
The number of reflection intensities between the measurement of
standard reflection intensities.
diffrn_standards.interval_time
The time in minutes between the measurement of standard
reflection intensities.
diffrn_standards.number
The number of unique standard reflections used during the
measurement of the diffraction intensities.
diffrn_standards.scale_sigma
The standard uncertainty (estimated standard deviation) of
the individual mean standard scales applied to the intensity
data.
diffrn_standards.scale_u
The standard uncertainty of the individual mean
standard scales applied to the intensity data.
diffrn_standards.diffrn_id
This data item is a pointer to attribute id in category diffrn in the DIFFRN
category.
em_2d_crystal_entity
Data items in the EM_2D_CRYSTAL_ENTITY category record
the symmetry details of a 2D crystal assembly component.
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
em_2d_crystal_entityCategory
This property indicates that datablock
has a category element em_2d_crystal_entity.
em_2d_crystal_entityItem
Abstract Datatype property for em_2d_crystal_entity items.
reference_to_em_2d_crystal_entity
cross-reference to em_2d_crystal_entity
em_2d_crystal_entity.angle_alpha
Unit-cell angle alpha of the reported structure, in degrees.
em_2d_crystal_entity.angle_beta
Unit-cell angle beta of the reported structure, in degrees.
em_2d_crystal_entity.angle_gamma
Unit-cell angle gamma of the reported structure, in degrees.
em_2d_crystal_entity.details
Any other details
This is a 2-D crystal.
em_2d_crystal_entity.length_a
Unit-cell length a corresponding to the structure reported, in Angstroms.
em_2d_crystal_entity.length_b
Unit-cell length b corresponding to the structure reported, in Angstroms.
em_2d_crystal_entity.length_c
Unit-cell length a corresponding to the structure reported, in Angstroms.
P 1
P 2 1
P 1 2
P 1 21
C 1 2
P 2 2 2
P 2 2 21
P 2 21 21
C 2 2 2
P 4
P 4 2 2
P 4 21 2
P 3
P 3 1 2
P 3 2 1
P 6
P 6 2 2
The 17 plane groups are classified as oblique, rectangular, square, and hexagonal.
To describe the symmetry of 2D crystals of biological molecules,
the plane groups are expanded to their equivalent noncentrosymmetric space groups.
The 2D crystal plane corresponds to the 'ab' plane of the space group.
.
Enumerated space group descriptions include the plane group number in parentheses,
the H-M plane group symbol, and the plane group class.
em_2d_crystal_entity.entity_assembly_id
The value of attribute entity_assembly_id in category em_2d_crystal_entity identifies
an assembly component with 2d crystal symmetry.
This data item is a pointer to attribute id in category em_entity_assembly in the
EM_ENTITY_ASSEMBLY category.
em_2d_crystal_entity.id
The value of attribute id in category em_2d_crystal_entity must uniquely identify
a set of the crystal parameters for this assembly component.
em_2d_crystal_grow
Data items in the EM_2D_CRYSTAL_GROW category
record details of growth conditions for 2d crystal samples.
Example 1 - based on PDB entry 1AT9 and laboratory records for the
structure corresponding to PDB entry 1DYL
<PDBx:em_2d_crystal_growCategory>
<PDBx:em_2d_crystal_grow id="1">
<PDBx:apparatus></PDBx:apparatus>
<PDBx:atmosphere>room air</PDBx:atmosphere>
<PDBx:buffer_id>2</PDBx:buffer_id>
<PDBx:citation_id>2</PDBx:citation_id>
<PDBx:details>on grid</PDBx:details>
<PDBx:mean_2d_crystal_size></PDBx:mean_2d_crystal_size>
<PDBx:method></PDBx:method>
<PDBx:number_2d_crystals>129</PDBx:number_2d_crystals>
<PDBx:pH>5.2</PDBx:pH>
<PDBx:temp>18</PDBx:temp>
<PDBx:time></PDBx:time>
</PDBx:em_2d_crystal_grow>
</PDBx:em_2d_crystal_growCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
em_2d_crystal_growCategory
This property indicates that datablock
has a category element em_2d_crystal_grow.
em_2d_crystal_growItem
Abstract Datatype property for em_2d_crystal_grow items.
reference_to_em_2d_crystal_grow
cross-reference to em_2d_crystal_grow
em_2d_crystal_grow.apparatus
The type of the apparatus used for growing the crystals.
Langmuir trough
em_2d_crystal_grow.atmosphere
The type of atmosphere in which crystals were grown.
room air
em_2d_crystal_grow.buffer_id
This data item is a pointer to attribute id in category em_buffer in the
BUFFER category.
em_2d_crystal_grow.citation_id
This data item is a pointer to attribute id
in category citation in the CITATION category.
em_2d_crystal_grow.details
Any additional items concerning 2d crystal growth.
em_2d_crystal_grow.mean_2d_crystal_size
The approximate size (microns squared) of 2d crystals imaged.
em_2d_crystal_grow.method
The method used for growing the crystals.
lipid monolayer
em_2d_crystal_grow.number_2d_crystals
The number of 2d crystals imaged.
em_2d_crystal_grow.pH
the pH value used for growing the crystals.
4.7
em_2d_crystal_grow.temp
The value of the temperature in degrees Kelvin used for
growing the crystals.
293
em_2d_crystal_grow.time
The length of time required to grow the crystals.
approximately 2 days
em_2d_crystal_grow.id
The value of attribute crystal_id
in category em_2d_crystal_grow must uniquely identify the sample 2d crystal.
em_2d_projection_selection
Data items in the EM_2D_PROJECTION_SELECTION category
record details of images from scanned micrographs and the
number of particles selected from a scanned set of micrographs.
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<PDBx:em_2d_projection_selectionCategory>
<PDBx:em_2d_projection_selection entry_id="1">
<PDBx:citation_id>1</PDBx:citation_id>
<PDBx:details></PDBx:details>
<PDBx:method>INTERACTIVE</PDBx:method>
<PDBx:num_particles>5267</PDBx:num_particles>
<PDBx:software_name>1</PDBx:software_name>
</PDBx:em_2d_projection_selection>
</PDBx:em_2d_projection_selectionCategory>
0
1
0
1
0
1
0
1
0
1
1
em_2d_projection_selectionCategory
This property indicates that datablock
has a category element em_2d_projection_selection.
em_2d_projection_selectionItem
Abstract Datatype property for em_2d_projection_selection items.
reference_to_em_2d_projection_selection
cross-reference to em_2d_projection_selection
em_2d_projection_selection.citation_id
This data item is a pointer to attribute id in category citation in the
CITATION category.
em_2d_projection_selection.details
Any additional details used for selecting observed assemblies.
negative monitor contrast facilitated particle picking
em_2d_projection_selection.method
The method used for selecting observed assemblies.
particles picked interactively from monitor
em_2d_projection_selection.num_particles
The number of particles selected from the projection set of images.
840
em_2d_projection_selection.software_name
This data item is a pointer to attribute name in category software in the
SOFTWARE category.
em_2d_projection_selection.entry_id
The value of attribute entry_id in category em_2d_projection_selection points to
the ENTRY category.
em_3d_fitting
Data items in the 3D_FITTING category
record details of the method of fitting atomic
coordinates from a PDB file into a 3d-em
volume map file
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<PDBx:em_3d_fittingCategory>
<PDBx:em_3d_fitting entry_id="1DYL" id="1">
<PDBx:details> THE CRYSTAL STRUCTURE OF THE CAPSID
PROTEIN FROM CHOI ET AL (1997) PROTEINS 3 27:345-359
(SUBUNIT A OF PDB FILE 1VCQ) WAS PLACED INTO THE CRYO-EM
DENSITY MAP. THE CAPSID PROTEIN WAS FIRST MANUALLY POSITIONED
INTO THE CRYO-EM DENSITY CORRESPONDING TO POSITIONS OF THE
FOUR INDEPENDENT MONOMER DENSITIES BETWEEN THE INNER LEAFLET
OF THE BILAYER AND THE RNA. THESE POSITIONS WERE THEN REFINED
BY RIGID BODY REFINEMENT IN REAL SPACE WITH THE PROGRAM EMFIT
(CHENG ET AL. 1995, CELL 80, 621-630). THE QUALITY OF THE FIT
CAN BE SEEN FROM THE MAP DENSITY WITHIN THE PROTEIN. ALL 4563
ATOMS ARE IN DENSITY OF AT LEAST 4 SIGMA (96.73) ABOVE THE
AVERAGE (512.04), 1167 ATOMS ARE IN DENSITY BETWEEN 4 AND 5
SIGMA, 3174 ATOMS ARE IN DENSITY BETWEEN 5 AND 6 SIGMA, AND 222
ATOMS ARE IN DENSTY OF 6 SIGMA OR ABOVE. THE VARIATION IN
DENSITY OVER THE FITTED PROTEIN CAN BE VISUALIZED WITH THE
PSEUDO TEMPERATURE FACTOR. THE DENSITY VALUE AT EACH ATOM IS
GIVEN IN THE 8TH COLUM (USUALLY THE OCCUPANCY) AS THE NUMBER
OF STANDARD DEVIATION ABOVE BACKGROUND. COLUMN NINE (USUALLY
THE TEMPERATURE FACTOR) CONTAINS THE VALUE OF THE RELATIVE
DENSITY WITHIN THE FITTED PROTEIN SCALED LINEARLY SO THAT THE
MINIMUM DENSITY IS 100.0 AND THE MAXIMUM DENSITY IS 1.0. THE
ATOMS THAT LIE IN THE LOWER DENSITY REGIONS WILL HAVE THE
HIGHEST PSEUDO TEMPERATURE FACTORS. </PDBx:details>
<PDBx:method>AUTOMATIC</PDBx:method>
<PDBx:overall_b_value></PDBx:overall_b_value>
<PDBx:ref_protocol>RIGID BODY REFINEMENT</PDBx:ref_protocol>
<PDBx:ref_space>REAL</PDBx:ref_space>
<PDBx:software_name>1</PDBx:software_name>
<PDBx:target_criteria>R-FACTOR</PDBx:target_criteria>
</PDBx:em_3d_fitting>
</PDBx:em_3d_fittingCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
em_3d_fittingCategory
This property indicates that datablock
has a category element em_3d_fitting.
em_3d_fittingItem
Abstract Datatype property for em_3d_fitting items.
reference_to_em_3d_fitting
cross-reference to em_3d_fitting
em_3d_fitting.details
Any additional details regarding fitting of atomic
coordinates into the 3d-em volume.
Initial local fitting was done using Chimera and then NMFF was used for flexible fitting.
em_3d_fitting.method
The method used to fit atomic coordinates
into the 3dem reconstructed map.
Local refinement, Flexible fitting
em_3d_fitting.overall_b_value
The overall B (temperature factor) value for the 3d-em volume.
200
em_3d_fitting.ref_protocol
The type of protocol used in the refinement.
rigid body
REAL
RECIPROCAL
A flag to indicate whether fitting was carried out in real
or reciprocal refinement space.
Real
Reciprocal
em_3d_fitting.software_name
The software used for fitting atomic coordinates to the map.
Situs, NMFF, YUP.scx, etc.
em_3d_fitting.target_criteria
The quality of fit of the atomic coordinates into the
3dem volume map.
Cross-correlation coefficient
em_3d_fitting.entry_id
This data item is a pointer to _entry_id in
the ENTRY category.
em_3d_fitting.id
The value of attribute id in category em_3d_fitting must uniquely identify
a fitting procedure of atomic coordinates
into 3dem reconstructed volume map.
em_3d_fitting_list
Data items in the 3D_FITTING_LIST category
lists the methods of fitting atomic coordinates from a PDB file
into a 3d-em volume map file
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<PDBx:em_3d_fitting_listCategory>
<PDBx:em_3d_fitting_list _3d_fitting_id="l" id="1">
<PDBx:pdb_chain_id></PDBx:pdb_chain_id>
<PDBx:pdb_entry_id>1VCQ</PDBx:pdb_entry_id>
</PDBx:em_3d_fitting_list>
</PDBx:em_3d_fitting_listCategory>
0
1
0
1
1
1
em_3d_fitting_listCategory
This property indicates that datablock
has a category element em_3d_fitting_list.
em_3d_fitting_listItem
Abstract Datatype property for em_3d_fitting_list items.
reference_to_em_3d_fitting_list
cross-reference to em_3d_fitting_list
em_3d_fitting_list.pdb_chain_id
The chain id for the entry used in fitting.
em_3d_fitting_list.pdb_entry_id
The PDB code for the entry used in fitting.
PDB entry 1EHZ
em_3d_fitting_list._3d_fitting_id
The value of attribute 3d_fitting_id in category em_3d_fitting_list is a pointer
to attribute id in category em_3d_fitting in the 3d_fitting category
em_3d_fitting_list.id
This data item is a unique identifier.
em_3d_reconstruction
Data items in the EM_3D_RECONSTRUCTION category
record details of the 3D reconstruction procedure from 2D projections.
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<PDBx:em_3d_reconstructionCategory>
<PDBx:em_3d_reconstruction entry_id="1DYL" id="1">
<PDBx:actual_pixel_size>2.52</PDBx:actual_pixel_size>
<PDBx:citation_id>1</PDBx:citation_id>
<PDBx:ctf_correction_method></PDBx:ctf_correction_method>
<PDBx:details></PDBx:details>
<PDBx:method>CROSS-COMMON LINES</PDBx:method>
<PDBx:nominal_pixel_size>2.64</PDBx:nominal_pixel_size>
<PDBx:resolution>9</PDBx:resolution>
<PDBx:resolution_method></PDBx:resolution_method>
</PDBx:em_3d_reconstruction>
</PDBx:em_3d_reconstructionCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
em_3d_reconstructionCategory
This property indicates that datablock
has a category element em_3d_reconstruction.
em_3d_reconstructionItem
Abstract Datatype property for em_3d_reconstruction items.
reference_to_em_3d_reconstruction
cross-reference to em_3d_reconstruction
em_3d_reconstruction.actual_pixel_size
The actual pixel size of projection set of images.
2.8
5.76
em_3d_reconstruction.citation_id
This data item is a pointer to attribute id in category citation in the
CITATION category.
em_3d_reconstruction.ctf_correction_method
The CTF-correction method.
The Contrast Transfer Function CTF compensation for low contrast
specimens (e.g. frozen-hydrated), for which phase contrast is the only
significant mechanism, then higher defocus levels must be used to
achieve any significant transfer, and several images at different
focus levels must be combined to complete the information lost from
the transfer gaps of any one image. The CTF correction can be applied
to each extracted particle separately or to the whole micrograph after
digitisation. The simplest level of compensation is to reverse phases
at the negative lobes of the CTF.
The volumes were CTF-corrected in defocus groups, with an average of approximately 999 individual images per group
em_3d_reconstruction.details
Any additional details used in the 3d reconstruction.
a modified version of SPIDER program was used for the reconstruction
em_3d_reconstruction.euler_angles_details
euler angles details
em_3d_reconstruction.magnification_calibration
The magnification calibration method for the 3d reconstruction.
TMV images
em_3d_reconstruction.method
The algorithm method used for the 3d-reconstruction.
cross-common lines
polar Fourier transform (PFT)
em_3d_reconstruction.nominal_pixel_size
The nominal pixel size of the projection set of images.
3.11
6.78
em_3d_reconstruction.num_class_averages
This item was correspondence to two type of em dataset
processing_emDataSet_singleParticle.numClassAverages
processing_emDataSet_icosahedral.numClassAverages
em_3d_reconstruction.num_particles
The number of particles used in the 3d reconstruction
em_3d_reconstruction.resolution
The final resolution (in angstroms)of the 3d reconstruction.
8.9
10.0
em_3d_reconstruction.resolution_method
The method used to determine the final resolution
of the 3d reconstruction.
The Fourier Shell Correlation criterion as a measure of
resolution is based on the concept of splitting the (2D)
data set into two halves; averaging each and comparing them
using the Fourier Ring Correlation (FRC) technique.
FSC at 0.5 cut-off
em_3d_reconstruction.software
software name
em_3d_reconstruction.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
em_3d_reconstruction.id
The value of attribute id in category em_3d_reconstruction must
uniquely identify the 3d reconstruction.
em_assembly
Data items in the EM_ASSEMBLY category record details
about the type of complex assembly that describes the
nature of the sample studied.
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<PDBx:em_assemblyCategory>
<PDBx:em_assembly entry_id="1DYL" id="1">
<PDBx:aggregation_state>PARTICLE</PDBx:aggregation_state>
<PDBx:composition>virus</PDBx:composition>
<PDBx:details></PDBx:details>
<PDBx:mol_wt_exp></PDBx:mol_wt_exp>
<PDBx:mol_wt_method></PDBx:mol_wt_method>
<PDBx:mol_wt_theo></PDBx:mol_wt_theo>
<PDBx:name>virus</PDBx:name>
<PDBx:num_components>1</PDBx:num_components>
</PDBx:em_assembly>
</PDBx:em_assemblyCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
em_assemblyCategory
This property indicates that datablock
has a category element em_assembly.
em_assemblyItem
Abstract Datatype property for em_assembly items.
reference_to_em_assembly
cross-reference to em_assembly
2D CRYSTAL
3D CRYSTAL
INDIVIDUAL STRUCTURE
FILAMENT
ICOSAHEDRAL
PARTICLE
TISSUE
CELL
A description of the aggregation state of the assembly.
2D CRYSTAL
3D CRYSTAL
FILAMENT
PARTICLE
TISSUE
CELL
em_assembly.composition
The known composition of the assembly.
em_assembly.details
A description of any additional details
describing the observed sample.
This sample was monodisperse.
em_assembly.mol_wt_exp
The value (in megadaltons) of the experimentally
determined molecular weight of the assembly.
em_assembly.mol_wt_method
The method used in determining
the molecular weight.
em_assembly.mol_wt_theo
The value (in megadaltons) of the theoretically
determined molecular weight of the assembly.
em_assembly.name
The name of the assembly of observed complexes.
Fab Fragment of Mab1-Ia monoclonal antibody bound to Human Rhinovirus1h Nim-Ia Site
em_assembly.num_components
The number of components of the biological assembly.
em_assembly.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
em_assembly.id
The value of attribute id in category em_assembly must uniquely identify
a collection of observed complexes.
em_buffer
Data items in the BUFFER category
record details of the sample buffer.
0
1
0
1
1
em_bufferCategory
This property indicates that datablock
has a category element em_buffer.
em_bufferItem
Abstract Datatype property for em_buffer items.
reference_to_em_buffer
cross-reference to em_buffer
em_buffer.details
Additional details about the buffer.
20mM NaCl, 10mM Tris-HCL,1mM MgCl2,1mM
em_buffer.name
The name of the buffer.
Polymix buffer
em_buffer.id
The value of attribute id in category em_buffer must
uniquely identify the sample buffer.
em_buffer_components
Constituents of buffer in sample
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<PDBx:em_buffer_componentsCategory>
<PDBx:em_buffer_components buffer_id="1" id="1">
<PDBx:conc>4 </PDBx:conc>
<PDBx:details></PDBx:details>
<PDBx:name>NaCl</PDBx:name>
<PDBx:volume>0.200 </PDBx:volume>
</PDBx:em_buffer_components>
<PDBx:em_buffer_components buffer_id="1" id="2">
<PDBx:conc>100</PDBx:conc>
<PDBx:details></PDBx:details>
<PDBx:name>Acetic Acid</PDBx:name>
<PDBx:volume>0.047 </PDBx:volume>
</PDBx:em_buffer_components>
<PDBx:em_buffer_components buffer_id="1" id="3">
<PDBx:conc>neat</PDBx:conc>
<PDBx:details></PDBx:details>
<PDBx:name>water</PDBx:name>
<PDBx:volume>0.700 </PDBx:volume>
</PDBx:em_buffer_components>
</PDBx:em_buffer_componentsCategory>
0
1
0
1
0
1
0
1
1
1
em_buffer_componentsCategory
This property indicates that datablock
has a category element em_buffer_components.
em_buffer_componentsItem
Abstract Datatype property for em_buffer_components items.
reference_to_em_buffer_components
cross-reference to em_buffer_components
em_buffer_components.conc
The millimolar concentration of buffer component.
200
em_buffer_components.details
Any additional details to do with buffer composition.
pH adjusted with NaOH
em_buffer_components.name
The name of each buffer component.
Acetic acid
em_buffer_components.volume
The volume of buffer component.
0.200
em_buffer_components.buffer_id
This data item is a pointer to attribute id in category em_buffer in the BUFFER category.
em_buffer_components.id
The value of attribute id in category em_buffer_components must
uniquely identify a component of the buffer.
em_detector
Data items in the EM_DETECTOR category record details
of the image detector type.
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<PDBx:em_detectorCategory>
<PDBx:em_detector entry_id="1DYL" id="1">
<PDBx:details></PDBx:details>
<PDBx:detective_quantum_efficiency></PDBx:detective_quantum_efficiency>
<PDBx:type>KODAK SO163 FILM</PDBx:type>
</PDBx:em_detector>
</PDBx:em_detectorCategory>
0
1
0
1
0
1
1
1
em_detectorCategory
This property indicates that datablock
has a category element em_detector.
em_detectorItem
Abstract Datatype property for em_detector items.
reference_to_em_detector
cross-reference to em_detector
em_detector.details
Any additional information about the detection system.
Any other details regarding the detector.
em_detector.detective_quantum_efficiency
The detective_quantum_efficiency (DQE)is defined as the
square of the signal-to-noise ratio in the recording device
divided by the square of the signal-to-ratio in the electron beam:
(SIGNAL/NOISE)2 recording device
DQE = -------------------------------
(SIGNAL/NOISE)2 electron beam
A DQE value of 1 indicates a perfect recorder. "DQE = 0.25" menas
that the signal-to-noise ratio is reduced by half in the
recording step.
(0.5)**2
DQE = --------- = 0.25.
(1.0)**2
0.25
em_detector.type
The detector type used for recording images.
Usually film or CCD camera.
KODAK SO163 FILM
GATAN 673
GATAN 676
GATAN 692
GATAN 794
GATAN 1000
GATAN 4000
TVIPS BIOCAM
TVIPS TEMCAM F214
TVIPS TEMCAM F224
TVIPS FASTSCAN F114
PROSCAN
AMT
em_detector.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
em_detector.id
The value of attribute id in category em_detector must uniquely identify
the detector used for imaging.
em_electron_diffraction
Data items in the EM_ELECTRON_DIFFRACTION category
record details about the electron diffraction data
from the electron crystallography experiment.
Example 1 - based on PDB entry 1TUB and laboratory records for the
structure corresponding to PDB entry 1TUB
<PDBx:em_electron_diffractionCategory>
<PDBx:em_electron_diffraction entry_id="1TUB" id="1">
<PDBx:details></PDBx:details>
<PDBx:num_diff_patterns></PDBx:num_diff_patterns>
<PDBx:num_structure_factors>12000</PDBx:num_structure_factors>
</PDBx:em_electron_diffraction>
</PDBx:em_electron_diffractionCategory>
1
1
0
1
0
1
1
1
em_electron_diffractionCategory
This property indicates that datablock
has a category element em_electron_diffraction.
em_electron_diffractionItem
Abstract Datatype property for em_electron_diffraction items.
reference_to_em_electron_diffraction
cross-reference to em_electron_diffraction
em_electron_diffraction.details
Details of the electron diffraction experiment
THE MODEL WAS DERIVED USING ELECTRON DIFFRACTION
AND IMAGE DATA FROM TWO DIMENSIONAL CRYSTALS OF TUBULIN
INDUCED BY THE PRESENCE OF ZN++ IONS.
WHAT FOLLOWS ARE THE COORDINATES FOR THE AB-TUBULIN DIMER
BOUND TO TAXOL AS OBTAINED BY ELECTRON CRYSTALLOGRAPHY OF
ZINC-INDUCED SHEETS. THIS IS THE UNREFINED MODEL, BUILT
INTO A RAW DENSITY MAP WHERE THE RESOLUTION IN THE PLANE
OF THE SHEET WAS 3.7 ANGSTROMS AND THAT PERPENDICULAR TO
THE SHEET ABOUT 4.8 ANGSTROMS. THE MODEL DOES NOT CONTAIN
MOST OF THE C-TERMINAL RESIDUES OF EITHER MONOMER WHICH
WERE DISORDERED IN THE MAP. THE LOOP BETWEEN HELIX H1 AND
STRAND S2, AND THAT BETWEEN H2 AND S3 ARE PRESENT FOR
COMPLETENESS BUT WERE BUILT INTO VERY WEAK DENSITY.
GIVEN THE LIMITED RESOLUTION OF THE MAP, THE CONFORMATION
OF THE SIDE CHAINS, ESPECIALLY THOSE CORRESPONDING TO
RESIDUES ON THE SURFACE OF THE DIMER, MUST BE TAKEN
CAUTIOUSLY. IN ADDITION, BECAUSE THIS IS AN UNREFINED
MODEL, CERTAIN GEOMETRY ERRORS MAY STILL BE PRESENT IN THE
STRUCTURE. PLEASE TAKE THIS INTO ACCOUNT WHEN
INTERPRETING YOUR OWN DATA BASED ON THE PRESENT TUBULIN
STRUCTURE. ALTHOUGH THE POSITION OF RESIDUES (WITH THE
EXCEPTION OF THOSE IN THE LOOPS MENTIONED ABOVE) SHOULD
NOT CHANGE SIGNIFICANTLY UPON REFINEMENT, DRAWING
INFORMATION AT THE LEVEL OF SIDE CHAIN CONFORMATION IS
CLEARLY NOT ADVISED. FINALLY, PLEASE NOTICE THAT THE
TAXOID IN THE MODEL IS THE TAXOL DERIVATIVE TAXOTERE.
1
em_electron_diffraction.num_diff_patterns
The number of diffraction patterns used from the electron
diffraction experiment.
em_electron_diffraction.num_structure_factors
The number of structure factors from the electron diffraction experiment.
12000
em_electron_diffraction.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
em_electron_diffraction.id
The value of attribute id in category electron_diffraction must
uniquely identify the electron diffraction experiment.
em_electron_diffraction_pattern
data items in the em_electron_diffraction_pattern category
record details about the pattern information
from the electron diffraction experiment.
example 1 - based on pdb entry 1tub and laboratory records for the
structure corresponding to pdb entry 1tub
<PDBx:em_electron_diffraction_patternCategory>
<PDBx:em_electron_diffraction_pattern entry_id="1TUB" id="1">
<PDBx:num_images_by_tilt_angle>4</PDBx:num_images_by_tilt_angle>
<PDBx:num_patterns_by_tilt_angle>1</PDBx:num_patterns_by_tilt_angle>
<PDBx:tilt_angle></PDBx:tilt_angle>
</PDBx:em_electron_diffraction_pattern>
</PDBx:em_electron_diffraction_patternCategory>
0
1
0
1
0
1
1
1
em_electron_diffraction_patternCategory
This property indicates that datablock
has a category element em_electron_diffraction_pattern.
em_electron_diffraction_patternItem
Abstract Datatype property for em_electron_diffraction_pattern items.
reference_to_em_electron_diffraction_pattern
cross-reference to em_electron_diffraction_pattern
em_electron_diffraction_pattern.num_images_by_tilt_angle
the number of images by tilt angle.
4
em_electron_diffraction_pattern.num_patterns_by_tilt_angle
the number of diffraction patterns by tilt angle.
1
em_electron_diffraction_pattern.tilt_angle
the tilt angle at which the diffraction pattern was obtained.
em_electron_diffraction_pattern.entry_id
this data item is a pointer to attribute id in category entry in the entry category.
em_electron_diffraction_pattern.id
the value of attribute id in category electron_diffraction_pattern must
uniquely identify the electron diffraction pattern experiment.
em_electron_diffraction_phase
data items in the em_electron_diffraction_phase category
record details about the phase information
from the electron diffraction experiment.
example 1 - based on pdb entry 1tub and laboratory records for the
structure corresponding to pdb entry 1tub
<PDBx:em_electron_diffraction_phaseCategory>
<PDBx:em_electron_diffraction_phase entry_id="1TUB" id="1">
<PDBx:d_res_high>4</PDBx:d_res_high>
<PDBx:highest_resolution_shell_error></PDBx:highest_resolution_shell_error>
<PDBx:overall_error></PDBx:overall_error>
<PDBx:rejection_criteria_error></PDBx:rejection_criteria_error>
<PDBx:residual></PDBx:residual>
</PDBx:em_electron_diffraction_phase>
</PDBx:em_electron_diffraction_phaseCategory>
0
1
0
1
0
1
0
1
0
1
1
1
em_electron_diffraction_phaseCategory
This property indicates that datablock
has a category element em_electron_diffraction_phase.
em_electron_diffraction_phaseItem
Abstract Datatype property for em_electron_diffraction_phase items.
reference_to_em_electron_diffraction_phase
cross-reference to em_electron_diffraction_phase
em_electron_diffraction_phase.d_res_high
the highest resolution d-value for the electron diffraction experiment.
5
em_electron_diffraction_phase.highest_resolution_shell_error
the highest resolution shell error in degrees.
em_electron_diffraction_phase.overall_error
the overall phase error in degrees.
em_electron_diffraction_phase.rejection_criteria_error
the rejection criteria (phase error) in degrees.
em_electron_diffraction_phase.residual
the phase residual value for the electron diffraction experiment.
em_electron_diffraction_phase.entry_id
this data item is a pointer to attribute id in category entry in the entry category.
em_electron_diffraction_phase.id
the value of attribute id in category electron_diffraction_phase must
uniquely identify the electron diffraction phase experiment.
em_entity_assembly
Data items in the EM_ENTITY_ASSEMBLY category
record details about each component of
the complex.
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<PDBx:em_entity_assemblyCategory>
<PDBx:em_entity_assembly assembly_id="1" id="1">
<PDBx:type>VIRUS</PDBx:type>
</PDBx:em_entity_assembly>
</PDBx:em_entity_assemblyCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
em_entity_assemblyCategory
This property indicates that datablock
has a category element em_entity_assembly.
em_entity_assemblyItem
Abstract Datatype property for em_entity_assembly items.
reference_to_em_entity_assembly
cross-reference to em_entity_assembly
em_entity_assembly.details
Additional details about the component.
Fab fragment generated by proteolytic cleavage of LA2 IgG antibody.
em_entity_assembly.ebi_cell
The cell from which the component was
obtained.
CHO
HELA
3T3
em_entity_assembly.ebi_cellular_location
The cellular location of the component.
cytoplasm
endoplasmic reticulum
plasma membrane
YES
NO
A flag to indicate whether the component is engineered.
em_entity_assembly.ebi_expression_system
The expression system used to produce the component.
eschericia coli
saccharomyces cerevisiae
em_entity_assembly.ebi_expression_system_plasmid
The plasmid used in the expression system used to produce the component.
pBR322
pMB9
em_entity_assembly.ebi_organelle
The organelle from which the component was
obtained.
golgi
mitochondrion
cytoskeleton
em_entity_assembly.ebi_organism_common
The common name of the species of the natural organism from which
the component was obtained.
em_entity_assembly.ebi_organism_scientific
The species of the natural organism from which the component
was obtained.
em_entity_assembly.ebi_strain
The strain of the natural organism from which the component was
obtained, if relevant.
DH5a
BMH 71-18
em_entity_assembly.ebi_tissue
The tissue of the natural organism from which the component was
obtained.
heart
liver
eye lens
em_entity_assembly.go_id
The Gene Ontology (GO) identifier for the component.
The GO id is the appropriate identifier used by the Gene Ontology
Consortium. Reference: Nature Genetics vol 25:25-29 (2000).
GO:0005876
GO:0015630
em_entity_assembly.ipr_id
The InterPro (IPR) identifier for the component.
The IPR id is the appropriate identifier used by the Interpro Resource.
Reference: Nucleic Acid Research vol 29(1):37-40(2001).
001304
002353
YES
NO
mutant flag
em_entity_assembly.name
The name of the component of the observed assembly.
messenger RNA
initiation factor 2
GroEL
antibody Fab fragment
em_entity_assembly.number_of_copies
number of copies
em_entity_assembly.oligomeric_details
oligomeric details
em_entity_assembly.synonym
Alternative name of the component.
FADV-1
VIRUS
PROTEIN
NUCLEIC ACID
LIGAND
LABEL
CELLULAR COMPONENT
RIBOSOME
A description of types of components of the
assembly of the biological structure.
em_entity_assembly.assembly_id
This data item is a pointer to attribute id in category em_assembly in the
ASSEMBLY category.
em_entity_assembly.id
The value of attribute id in category em_entity_assembly must uniquely identify
each of the components of the complex.
em_entity_assembly_list
Data items in the EM_ENTITY_ASSEMBLY_LIST category record details
of the structural elements in each component.
Example 1 - microtubule
<PDBx:em_entity_assembly_listCategory>
<PDBx:em_entity_assembly_list entity_assembly_id="1" entity_id="1" id="1">
<PDBx:number_of_copies>2</PDBx:number_of_copies>
<PDBx:oligomeric_details>DIMER</PDBx:oligomeric_details>
</PDBx:em_entity_assembly_list>
</PDBx:em_entity_assembly_listCategory>
0
1
0
1
1
1
1
em_entity_assembly_listCategory
This property indicates that datablock
has a category element em_entity_assembly_list.
em_entity_assembly_listItem
Abstract Datatype property for em_entity_assembly_list items.
reference_to_em_entity_assembly_list
cross-reference to em_entity_assembly_list
em_entity_assembly_list.number_of_copies
The number of copies of the entity.
em_entity_assembly_list.oligomeric_details
The oligomeric state of the entity.
em_entity_assembly_list.entity_assembly_id
This data item is a pointer to attribute id in category em_entity_assembly in
the ENTITY_ASSEMBLY category.
em_entity_assembly_list.entity_id
A pointer to entity id.
em_entity_assembly_list.id
The value of attribute id in category em_entity_assembly_list must uniquely identify
the component.
em_euler_angle_distribution
Data items in the EM_EULER_ANGLE_DISTRIBUTION category
record details of assignment of Euler angles for projection
sets of particles.
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<PDBx:em_euler_angle_distributionCategory>
<PDBx:em_euler_angle_distribution entry_id="1DYL" id="1">
<PDBx:alpha></PDBx:alpha>
<PDBx:beta></PDBx:beta>
<PDBx:details></PDBx:details>
<PDBx:gamma></PDBx:gamma>
</PDBx:em_euler_angle_distribution>
</PDBx:em_euler_angle_distributionCategory>
0
1
0
1
0
1
0
1
1
1
em_euler_angle_distributionCategory
This property indicates that datablock
has a category element em_euler_angle_distribution.
em_euler_angle_distributionItem
Abstract Datatype property for em_euler_angle_distribution items.
reference_to_em_euler_angle_distribution
cross-reference to em_euler_angle_distribution
em_euler_angle_distribution.alpha
The euler-alpha angle assignment.
90
em_euler_angle_distribution.beta
The euler-beta angle assignment.
90
em_euler_angle_distribution.details
Any additional details of the euler angles distribution and assignment.
em_euler_angle_distribution.gamma
The euler-gamma angle assignment.
0
em_euler_angle_distribution.entry_id
The value of attribute entry_id in category em_euler_angle_distribution is a pointer
to the ENTRY category.
em_euler_angle_distribution.id
The value of attribute id in category em_euler_angle_distribution must
uniquely identify the euler angle assignments of
the projection set used in the final reconstruction.
em_experiment
Data items in the EM_EXPERIMENT category provide
high-level classification of the EM experiment.
Example 1 - based on PDB entry 1EG0
<PDBx:em_experimentCategory>
<PDBx:em_experiment entry_id="1EG0">
<PDBx:reconstruction_method>SINGLE PARTICLE</PDBx:reconstruction_method>
<PDBx:specimen_type>VITREOUS ICE (CRYO EM)</PDBx:specimen_type>
</PDBx:em_experiment>
</PDBx:em_experimentCategory>
0
1
0
1
1
em_experimentCategory
This property indicates that datablock
has a category element em_experiment.
em_experimentItem
Abstract Datatype property for em_experiment items.
reference_to_em_experiment
cross-reference to em_experiment
SINGLE PARTICLE
HELICAL
CRYSTALLOGRAPHY
TOMOGRAPHY
The reconstruction method used in the EM experiment.
em_experiment.specimen_type
The specimen type used in the EM experiment.
VITREOUS ICE (CRYO EM)
NEGATIVE STAIN
FREEZE SUBSTITUTION
em_experiment.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
em_helical_entity
0
1
0
1
0
1
0
1
0
1
0
1
1
1
em_helical_entityCategory
This property indicates that datablock
has a category element em_helical_entity.
em_helical_entityItem
Abstract Datatype property for em_helical_entity items.
reference_to_em_helical_entity
cross-reference to em_helical_entity
em_helical_entity.angular_rotation_per_subunit
The angular rotation per helical subunit in degrees.
-34.616000
em_helical_entity.axial_rise_per_subunit
The axial rise per subunit in the helical assembly.
17.400000
em_helical_entity.axial_symmetry
n-fold symmetry along the filament helix axis.
1
5
7
em_helical_entity.details
Any other details regarding the helical assembly
Dihedral symmetry
YES
NO
Value should be YES if a the filament has two-fold symmetry perpendicular to the helical axis.
em_helical_entity.hand
Handedness of the helix: right handed or left handed
Right
Left
em_helical_entity.entity_assembly_id
The value of attribute entity_assembly_id
in category em_helical_entity identifies a particular assembly component.
This data item is a pointer to attribute id
in category entity_assembly in the EM_ENTITY_ASSEMBLY category.
em_helical_entity.id
The value of attribute id in category em_helical_entity must uniquely identify
a set of the filament parameters for this assembly component.
em_icos_virus_shells
Data items in the EM_ICOS_VIRUS_SHELLS category record details
of the viral shell number, diameter of each shell and triangulation number.
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<PDBx:em_icos_virus_shellsCategory>
<PDBx:em_icos_virus_shells id="1" virus_entity_id="1">
<PDBx:shell_diameter>400</PDBx:shell_diameter>
<PDBx:triangulation_num>4</PDBx:triangulation_num>
</PDBx:em_icos_virus_shells>
</PDBx:em_icos_virus_shellsCategory>
0
1
0
1
1
1
em_icos_virus_shellsCategory
This property indicates that datablock
has a category element em_icos_virus_shells.
em_icos_virus_shellsItem
Abstract Datatype property for em_icos_virus_shells items.
reference_to_em_icos_virus_shells
cross-reference to em_icos_virus_shells
em_icos_virus_shells.shell_diameter
The value of the diameter (in angstroms) for each
protein shell of the virus.
em_icos_virus_shells.triangulation_num
The triangulation number (T number) is a geometric and abstract
concept that does not correspond to the structural components of
an individul virus.
It refers to the organisation of the geometric figure.
The triangulation number, T is given by the following relationship:
T= h*2 + hk +k*2, where h and k are positive integers which define the
position of the five-fold vertex on the original hexagonal net.
4
em_icos_virus_shells.id
The value of attribute id in category em_em_icos_virus_shells must uniquely identify
the number and diameter of each virus protein shell and its
triangulation number.
em_icos_virus_shells.virus_entity_id
The value of attribute virus_entity_id in category em_icos_virus_shells is
a pointer to attribute id in category em_virus_entity in the VIRUS_ENTITY
category.
em_image_scans
Data items in the EM_IMAGE_SCANS category record details
of the image scanning device (microdensitometer)
and parameters for digitization of the image.
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<PDBx:em_image_scansCategory>
<PDBx:em_image_scans entry_id="1DYL" id="2">
<PDBx:citation_id>1</PDBx:citation_id>
<PDBx:details></PDBx:details>
<PDBx:number_digital_images>48</PDBx:number_digital_images>
<PDBx:od_range></PDBx:od_range>
<PDBx:quant_bit_size></PDBx:quant_bit_size>
<PDBx:sampling_size></PDBx:sampling_size>
<PDBx:scanner_model></PDBx:scanner_model>
</PDBx:em_image_scans>
</PDBx:em_image_scansCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
em_image_scansCategory
This property indicates that datablock
has a category element em_image_scans.
em_image_scansItem
Abstract Datatype property for em_image_scans items.
reference_to_em_image_scans
cross-reference to em_image_scans
em_image_scans.citation_id
This data item is a pointer to attribute id
in category citation in the CITATION category.
em_image_scans.details
Any additional details about scanning images.
em_image_scans.number_digital_images
The number of images scanned and digitised.
em_image_scans.od_range
The optical density range (OD=-log 10 transmission).
To the eye OD=1 appears light grey and OD=3 is opaque.
1.4
em_image_scans.quant_bit_size
The number of bits per pixel.
8
em_image_scans.sampling_size
The sampling step size (microns) set on the scanner.
ZEISS SCAI
EMIL 10
OPTRONICS
PERKIN ELMER
TEMSCAN
EIKONIX IEEE 488
NIKON COOLSCAN
NIKON SUPER COOLSCAN 9000
IMAGE SCIENCE PATCHWORK DENSITOMETER
PRIMESCAN
OTHER
The scanner model.
em_image_scans.entry_id
This data item is a pointer to attribute id in category entry in the
ENTRY category.
em_image_scans.id
The value of attribute id in category em_image_scans must uniquely identify
the images scanned.
em_imaging
Data items in the EM_IMAGING category record details about
the parameters used in imaging the sample in the electron microscope.
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<PDBx:em_imagingCategory>
<PDBx:em_imaging entry_id="1DYL" id="1">
<PDBx:accelerating_voltage>200</PDBx:accelerating_voltage>
<PDBx:calibrated_magnification></PDBx:calibrated_magnification>
<PDBx:citation_id>1</PDBx:citation_id>
<PDBx:date>1998-15-06</PDBx:date>
<PDBx:details></PDBx:details>
<PDBx:detector_distance></PDBx:detector_distance>
<PDBx:electron_dose></PDBx:electron_dose>
<PDBx:electron_source>FEG</PDBx:electron_source>
<PDBx:energy_filter></PDBx:energy_filter>
<PDBx:energy_window></PDBx:energy_window>
<PDBx:illumination_mode>bright field</PDBx:illumination_mode>
<PDBx:microscope_model>FEI/PHILIPS CM200 FEG</PDBx:microscope_model>
<PDBx:mode>low dose</PDBx:mode>
<PDBx:nominal_cs>2.0</PDBx:nominal_cs>
<PDBx:nominal_defocus_max>7600</PDBx:nominal_defocus_max>
<PDBx:nominal_defocus_min>975</PDBx:nominal_defocus_min>
<PDBx:nominal_magnification>50000</PDBx:nominal_magnification>
<PDBx:recording_temperature_maximum></PDBx:recording_temperature_maximum>
<PDBx:recording_temperature_minimum></PDBx:recording_temperature_minimum>
<PDBx:sample_support_id>1</PDBx:sample_support_id>
<PDBx:specimen_holder_model>gatan 626-0300</PDBx:specimen_holder_model>
<PDBx:specimen_holder_type>cryotransfer</PDBx:specimen_holder_type>
<PDBx:temperature>95</PDBx:temperature>
<PDBx:tilt_angle_max>0</PDBx:tilt_angle_max>
<PDBx:tilt_angle_min>0</PDBx:tilt_angle_min>
</PDBx:em_imaging>
</PDBx:em_imagingCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
0
1
0
1
0
1
0
1
0
1
1
1
em_imagingCategory
This property indicates that datablock
has a category element em_imaging.
em_imagingItem
Abstract Datatype property for em_imaging items.
reference_to_em_imaging
cross-reference to em_imaging
em_imaging.accelerating_voltage
A value of accelerating voltage (in kV) used for imaging.
300
em_imaging.astigmatism
astigmatism
em_imaging.calibrated_magnification
The magnification value obtained for a known standard just
prior to, during or just after the imaging experiment.
61200
em_imaging.citation_id
This data item is a pointer to attribute id in category citation in
the CITATION category.
em_imaging.date
Date (YYYY-MM-DD) of imaging experiment or the date at which
a series of experiments began.
2001-05-08
em_imaging.details
Any additional imaging details.
weak beam illumination
em_imaging.detector_distance
The camera length (in millimetres). The camera length is the
product of the objective focal length and the combined magnification
of the intermediate and projector lenses when the microscope is
operated in the diffraction mode.
em_imaging.detector_id
The value of attribute detector_id in category em_imaging must uniquely identify
the type of detector used in the experiment.
em_imaging.electron_beam_tilt_params
electron beam tilt params
em_imaging.electron_dose
The electron dose received by the specimen (electrons per square angstrom).
0.9
em_imaging.electron_source
The source of electrons. The electron gun.
FIELD EMISSION GUN
LAB6
TUNGSTEN HAIRPIN
SCHOTTKY FIELD EMISSION GUN
OTHER
em_imaging.energy_filter
The type of energy filter spectrometer apparatus.
FEI
em_imaging.energy_window
The energy filter range in electron volts (eV)set by spectrometer.
0 - 15
em_imaging.illumination_mode
The mode of illumination.
FLOOD BEAM
FLOOD BEAM LOW DOSE
SPOT SCAN
OTHER
em_imaging.microscope_id
This data item is a pointer to attribute id in category em_microscope in
the EM_MICROSCOPE category.
em_imaging.microscope_model
The name of the model of microscope.
HITACHI H8100
HITACHI HF2000
HITACHI HF2000-UHR
HITACHI H9000-UHR
HITACHI H9000-NAR
HITACHI 300KEV FEG
HITACHI HU1250
HITACHI H-1500
JEOL 2000EX
JEOL 2010HT
JEOL 2010UHR
JEOL 2010F
JEOL 3010HT
JEOL 3010UHR
JEOL KYOTO-3000SFF
JEOL 4000EX
JEOL HAREM
JEOL ARM-1000
JEOL KYOTO-1000
JEOL ARM-1250
FEI/PHILIPS CM120T
FEI/PHILIPS CM200T
FEI/PHILIPS CM20/ST
FEI/PHILIPS CM20/SOPHIE
FEI/PHILIPS CM200FEG/ST
FEI/PHILIPS CM20/UT
FEI/PHILIPS CM200FEG/UT
FEI/PHILIPS CM30/T
FEI/PHILIPS CM300FEG/T
FEI/PHILIPS CM300FEG/HE
FEI/PHILIPS CM30/ST
FEI/PHILIPS CM300FEG/ST
FEI/PHILIPS CM300FEG/UT
FEI TECNAI 12
FEI TECNAI 20
FEI TECNAI F20
FEI TECNAI F30
FEI MORGAGNI
em_imaging.mode
The mode of imaging.
BRIGHT FIELD
DARK FIELD
DIFFRACTION
OTHER
em_imaging.nominal_cs
The spherical aberration coefficient (Cs) in millimetres,
of the objective lens.
1.4
em_imaging.nominal_defocus_max
The maximum defocus value of the objective lens (in nanometres) used
to obtain the recorded images.
5000
em_imaging.nominal_defocus_min
The minimum defocus value of the objective lens (in nanometres) used
to obtain the recorded images.
1200
em_imaging.nominal_magnification
The magnification indicated by the microscope readout.
60000
em_imaging.recording_temperature_maximum
The specimen temperature maximum (degrees Kelvin) for the duration
of imaging.
em_imaging.recording_temperature_minimum
The specimen temperature minimum (degrees Kelvin) for the duration
of imaging.
em_imaging.sample_support_id
This data item is a pointer to attribute id in category em_sample_support in
the EM_SAMPLE_SUPPORT category.
em_imaging.scans_id
The value of attribute scans_id in category em_imaging must uniquely identify
the image_scans used in the experiment.
GATAN HELIUM
GATAN LIQUID NITROGEN
JEM3200FSC CRYOHOLDER
PHILIPS ROTATION HOLDER
HOME BUILD
JEOL
SIDE ENTRY, EUCENTRIC
OTHER
The name of the model of specimen holder used during imaging.
em_imaging.specimen_holder_type
The type of specimen holder used during imaging.
cryo
em_imaging.temperature
The mean specimen stage temperature (degrees Kelvin) during imaging
in the microscope.
70
em_imaging.tilt_angle_max
The maximum angle at which the specimen was tilted to obtain
recorded images.
70
em_imaging.tilt_angle_min
The minimum angle at which the specimen was tilted to obtain
recorded images.
-70
em_imaging.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
em_imaging.id
The value of attribute id in category em_imaging must uniquely identify
each imaging experiment.
em_sample_preparation
Data items in the EM_SAMPLE_PREPARATION category
record details of sample conditions prior to loading
onto grid support.
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<PDBx:em_sample_preparationCategory>
<PDBx:em_sample_preparation entry_id="1DYL" id="1">
<PDBx:_2d_crystal_grow_id></PDBx:_2d_crystal_grow_id>
<PDBx:buffer_id>1</PDBx:buffer_id>
<PDBx:ph>7.6</PDBx:ph>
<PDBx:sample_concentration>5</PDBx:sample_concentration>
<PDBx:support_id>1</PDBx:support_id>
</PDBx:em_sample_preparation>
</PDBx:em_sample_preparationCategory>
0
1
0
1
0
1
1
1
0
1
0
1
0
1
1
1
em_sample_preparationCategory
This property indicates that datablock
has a category element em_sample_preparation.
em_sample_preparationItem
Abstract Datatype property for em_sample_preparation items.
reference_to_em_sample_preparation
cross-reference to em_sample_preparation
em_sample_preparation._2d_crystal_grow_id
This data item is a pointer to attribute id
in category em_2d_crystal_grow in the 2D_CRYSTAL_GROW category.
em_sample_preparation.buffer_id
This data item is a pointer to attribute id in category em_buffer in the
BUFFER category.
em_sample_preparation.details
Details on the sample preparation
Selectively stained by injection of horseradish peroxidase,
embedded in Spurr's resin and cut into 2-3 um thick sections.
1
Enzyme Preparations. S. cerevisiae PDC was purified to near homogeneity
from baker's yeast by modification of a published procedure. Highly
purified E1 was obtained by resolution of PDC with 2 M NaCl at pH 7.3
followed by FPLC on a Superdex 200 column. The weight-average molecular
weight of the PDC was determined by light scattering measurement to be
~8 x 106. On the basis of the known molecular weight of the complex and
its component enzymes and the experimentally determined polypeptide chain
ratios of E2/BP/E3, we estimated that the subunit composition of the
S. cerevisiae PDC is ~24 E1 tetramers, 60 E2 monomers, 12 BP monomers,
and 8 E3 dimers. Sufficient E1 was added to a sample of the PDC
preparation to increase the molar ratio of E1/E2 core to 60:1.
This product is designated larger PDC or ~60 E1/E2 core PDC
2
embedment in vitreous ice.
3
Detergent-solubilized particles eluted from the cation-exchange
column were directly adsorbed for 1 min to parlodion carbon-coated
copper grids rendered hydrophilic by glow discharge at low pressure
in air. Grids were washed with 4 drops of double-distilled water
and stained with 2 drops of 0.75% uranyl formate. Images were recorded
on Eastman Kodak Co. SO-163 sheet film with a Hitachi H-7000
electron microscope operated at 100 kV. Electron micrographs of
single particles adsorbed to the carbon film were digitized using
a Leafscan-45 scanner (Leaf Systems, Inc., Westborough, MA).
4
em_sample_preparation.entity_assembly_id
This data item is a pointer to attribute id in category entity_assembly in the
entity_assembly category.
em_sample_preparation.ph
The pH value of the observed sample buffer.
5.5
em_sample_preparation.sample_concentration
The value of the concentration (mg per milliliter)
of the complex in the sample.
1.35
em_sample_preparation.support_id
This data item is a pointer to attribute id
in category em_sample_support in the EM_SAMPLE_SUPPORT category.
em_sample_preparation.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
em_sample_preparation.id
The value of attribute id in category em_sample_preparation must
uniquely identify the sample preparation.
em_sample_support
Data items in the EM_SAMPLE_SUPPORT category record details
of the electron microscope grid type, grid support film and pretreatment
of whole before sample is applied
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<PDBx:em_sample_supportCategory>
<PDBx:em_sample_support id="1">
<PDBx:citation_id>2</PDBx:citation_id>
<PDBx:details></PDBx:details>
<PDBx:film_material>HOLEY CARBON</PDBx:film_material>
<PDBx:grid_material>COPPER</PDBx:grid_material>
<PDBx:grid_mesh_size>400</PDBx:grid_mesh_size>
<PDBx:grid_type>MESH</PDBx:grid_type>
<PDBx:method></PDBx:method>
<PDBx:pretreatment>GLOW DISCHARGE</PDBx:pretreatment>
</PDBx:em_sample_support>
</PDBx:em_sample_supportCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
em_sample_supportCategory
This property indicates that datablock
has a category element em_sample_support.
em_sample_supportItem
Abstract Datatype property for em_sample_support items.
reference_to_em_sample_support
cross-reference to em_sample_support
em_sample_support.citation_id
This data item is a pointer to attribute id
in category citation in the CITATION category.
em_sample_support.details
A description of any additional details concerning the sample support.
This grid plus sample was kept at -170 deg C for a month before use
CARBON
FORMVAR PLUS CARBON
CELLULOSE ACETATE PLUS CARBON
PARLODION PLUS CARBON
HOLEY CARBON
The support material covering the em grid.
COPPER
COPPER/PALLADIUM
COPPER/RHODIUM
GOLD
NICKEL
PLATINUM
TUNGSTEN
TITANIUM
MOLYBDENUM
The name of the material from which the grid is made.
em_sample_support.grid_mesh_size
The value of the mesh size (per inch) of the em grid.
400
SLOT
APERTURE
DIAMOND
HEXAGONAL
A description of the grid type.
em_sample_support.method
A description of the method used to produce the support film.
1%formvar in chloroform cast on distilled water
em_sample_support.pretreatment
A description of the grid plus support film pretreatment.
glow-discharged for 30 sec in argon
em_sample_support.id
The value of attribute id in category em_sample_support must uniquely identify
the sample support.
em_single_particle_entity
Data items in the EM_SINGLE_PARTICLE_ENTITY category provide
the details of the symmetry for a single particle entity type.
Example 1 - based on PDB entry 1EG0
<PDBx:em_single_particle_entityCategory>
<PDBx:em_single_particle_entity entry_id="1EG0">
<PDBx:symmetry_type>ASYMMETRIC</PDBx:symmetry_type>
</PDBx:em_single_particle_entity>
</PDBx:em_single_particle_entityCategory>
Example 2 - based on PDB entry 2ZLE
<PDBx:em_single_particle_entityCategory>
<PDBx:em_single_particle_entity entry_id="2ZLE">
<PDBx:symmetry_type>MIXED SYMMETRY</PDBx:symmetry_type>
</PDBx:em_single_particle_entity>
</PDBx:em_single_particle_entityCategory>
0
1
1
em_single_particle_entityCategory
This property indicates that datablock
has a category element em_single_particle_entity.
em_single_particle_entityItem
Abstract Datatype property for em_single_particle_entity items.
reference_to_em_single_particle_entity
cross-reference to em_single_particle_entity
ASYMMETRIC
CYCLIC
DIHEDRAL
TETRAHEDRAL
OCTAHEDRAL
ICOSAHEDRAL
MIXED SYMMETRY
The single particle symmetry type.
em_single_particle_entity.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
em_virus_entity
Data items in the EM_VIRUS_ENTITY category record details
of the icosahedral virus.
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<PDBx:em_virus_entityCategory>
<PDBx:em_virus_entity entity_assembly_id="1" id="1">
<PDBx:empty>NO</PDBx:empty>
<PDBx:enveloped>YES</PDBx:enveloped>
<PDBx:ictvdb_id>00.073.0.01.023</PDBx:ictvdb_id>
<PDBx:virus_host_category>VERTERBRATES</PDBx:virus_host_category>
<PDBx:virus_host_species>HOMO SAPIENS</PDBx:virus_host_species>
<PDBx:virus_isolate>STRAIN</PDBx:virus_isolate>
<PDBx:virus_type>VIRUS</PDBx:virus_type>
</PDBx:em_virus_entity>
</PDBx:em_virus_entityCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
em_virus_entityCategory
This property indicates that datablock
has a category element em_virus_entity.
em_virus_entityItem
Abstract Datatype property for em_virus_entity items.
reference_to_em_virus_entity
cross-reference to em_virus_entity
em_virus_entity.details
Additional details about this virus entity
YES
NO
Flag to indicate if the virus is empty or not.
YES
NO
Flag to indicate if the virus is enveloped or not.
em_virus_entity.ictvdb_id
The International Committee on Taxonomy of Viruses
(ICTV) Taxon Identifier is the Virus Code used throughout the
ICTV database (ICTVdb). The ICTVdb id is the appropriate
identifier used by the International Committee on Taxonomy of Viruses
Resource. Reference: Virus Taxonomy, Academic Press (1999).
ISBN:0123702003.
NL-54
em_virus_entity.virus_host_category
The host category description for the virus.
ALGAE
ARCHAEA
BACTERIA(EUBACTERIA)
FUNGI
INVERTEBRATES
PLANTAE (HIGHER PLANTS)
PROTOZOA
VERTEBRATES
em_virus_entity.virus_host_growth_cell
The host cell from which the virus was isolated.
HELA
CHO
em_virus_entity.virus_host_species
The host species from which the virus was isolated.
homo sapiens
gallus gallus
STRAIN
SEROTYPE
SEROCOMPLEX
SUBSPECIES
SPECIES
OTHER
The isolate from which the virus was obtained.
em_virus_entity.virus_type
The type of virus.
VIRION
SATELLITE
PRION
VIROID
VIRUS-LIKE PARTICLE
em_virus_entity.entity_assembly_id
This data item is a pointer to attribute id in category em_virus_entity in the
ENTITY_ASSEMBLY category.
em_virus_entity.id
Is the unique identifier for VIRUS_ENTITY category.
em_vitrification
Data items in the EM_VITRIFICATION category
record details about the method and cryogen used in
rapid freezing of the sample on the grid prior to its
insertion in the electron microscope
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<PDBx:em_vitrificationCategory>
<PDBx:em_vitrification entry_id="1DYL" id="1">
<PDBx:citation_id>1</PDBx:citation_id>
<PDBx:cryogen_name>ETHANE</PDBx:cryogen_name>
<PDBx:details> SAMPLES WERE PREPARED AS THIN
LAYERS OF VITREOUS ICE AND
MAINTAINED AT NEAR LIQUID NITROGEN
TEMPERATURE IN THE ELECTRON MICROSCOPE
WITH A GATAN 626-0300 CRYOTRANSFER
HOLDER. </PDBx:details>
<PDBx:humidity>90</PDBx:humidity>
<PDBx:instrument></PDBx:instrument>
<PDBx:method>PLUNGE VITRIFICATION</PDBx:method>
<PDBx:sample_preparation_id>1</PDBx:sample_preparation_id>
<PDBx:temp>95</PDBx:temp>
<PDBx:time_resolved_state></PDBx:time_resolved_state>
</PDBx:em_vitrification>
</PDBx:em_vitrificationCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
em_vitrificationCategory
This property indicates that datablock
has a category element em_vitrification.
em_vitrificationItem
Abstract Datatype property for em_vitrification items.
reference_to_em_vitrification
cross-reference to em_vitrification
em_vitrification.citation_id
This data item is a pointer to attribute id in category citation in the
CITATION category.
HELIUM
NITROGEN
PROPANE
ETHANE
METHANE
FREON 22
FREON 12
OTHER
NONE
This is the name of the cryogen.
em_vitrification.details
Any additional details relating to vitrification.
Vitrification carried out in argon atmosphere.
em_vitrification.humidity
The humidity (%) in the vicinity of the vitrification process.
90
em_vitrification.instrument
The type of instrument used in the vitrification process.
Reichert plunger
em_vitrification.method
The procedure for vitrification.
blot for 2 seconds before plunging
em_vitrification.sample_preparation_id
This data item is a pointer to attribute id in category em_sample_preparation in the
EM_SAMPLE_PREPARATION category.
em_vitrification.temp
The temperature (in degrees Kelvin) at which vitrification took place.
4.2
em_vitrification.time_resolved_state
The length of time after an event effecting the sample that
vitrification was induced and a description of the event.
30 msec after spraying with effector'
em_vitrification.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
em_vitrification.id
The value of attribute id in category em_vitrification must uniquely identify
the vitrification procedure.
entity
Data items in the ENTITY category record details (such as
chemical composition, name and source) about the molecular
entities that are present in the crystallographic structure.
Items in the various ENTITY subcategories provide a full
chemical description of these molecular entities.
Entities are of three types: polymer, non-polymer and water.
Note that the water category includes only water; ordered
solvent such as sulfate ion or acetone would be described as
individual non-polymer entities.
The ENTITY category is specific to macromolecular CIF
applications and replaces the function of the CHEMICAL category
in the CIF core.
It is important to remember that the ENTITY data are not the
result of the crystallographic experiment; those results are
represented by the ATOM_SITE data items. ENTITY data items
describe the chemistry of the molecules under investigation
and can most usefully be thought of as the ideal groups to which
the structure is restrained or constrained during refinement.
It is also important to remember that entities do not correspond
directly to the enumeration of the contents of the asymmetric
unit. Entities are described only once, even in those structures
that contain multiple observations of an entity. The
STRUCT_ASYM data items, which reference the entity list,
describe and label the contents of the asymmetric unit.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:entityCategory>
<PDBx:entity id="1">
<PDBx:details> The enzymatically competent form of HIV
protease is a dimer. This entity
corresponds to one monomer of an active dimer.</PDBx:details>
<PDBx:formula_weight>10916</PDBx:formula_weight>
<PDBx:type>polymer</PDBx:type>
</PDBx:entity>
<PDBx:entity id="2">
<PDBx:details></PDBx:details>
<PDBx:formula_weight>762</PDBx:formula_weight>
<PDBx:type>non-polymer</PDBx:type>
</PDBx:entity>
<PDBx:entity id="3">
<PDBx:details></PDBx:details>
<PDBx:formula_weight>18</PDBx:formula_weight>
<PDBx:type>water</PDBx:type>
</PDBx:entity>
</PDBx:entityCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
entityCategory
This property indicates that datablock
has a category element entity.
entityItem
Abstract Datatype property for entity items.
reference_to_entity
cross-reference to entity
entity.details
A description of special aspects of the entity.
entity.formula_weight
Formula mass in daltons of the entity.
entity.pdbx_description
A description of the entity, with the name of the entity
in parenthesis.
Maps to PDB compound name.
DNA (5'-D(*GP*(CH3)CP*GP*(CH3)CP*GP*C)-3')
PROFLAVINE
PROTEIN (DEOXYRIBONUCLEASE I (E.C.3.1.21.1))
entity.pdbx_ec
Enzyme Commission (EC) number(s)
2.7.7.7
entity.pdbx_formula_weight_exptl
Experimentally determined formula mass in daltons of the entity
MASS SPEC
Method used to determine attribute pdbx_formula_weight_exptl in category entity.
MASS SPEC
entity.pdbx_fragment
Entity fragment description(s).
KLENOW FRAGMENT
REPLICASE OPERATOR HAIRPIN
C-TERMINAL DOMAIN
entity.pdbx_modification
Description(s) of any chemical or post-translational modifications
entity.pdbx_mutation
Details about any entity mutation(s).
Y31H
DEL(298-323)
entity.pdbx_number_of_molecules
A place holder for the number of molecules of the entity in
the entry.
1.0
2.0
3.0
entity.pdbx_parent_entity_id
An identifier for the parent entity if this entity
is part of a complex entity. For instance a chimeric
entity may be decomposed into several independent
chemical entities where each component entity was
obtained from a different source.
1
2
3
entity.pdbx_target_id
The value of attribute target_id in category entity points to a TARGETDB target idenitifier
from which this entity was generated.
nat
man
syn
The method by which the sample for the entity was produced.
Entities isolated directly from natural sources (tissues, soil
samples etc.) are expected to have further information in the
ENTITY_SRC_NAT category. Entities isolated from genetically
manipulated sources are expected to have further information in
the ENTITY_SRC_GEN category.
polymer
non-polymer
macrolide
water
Defines the type of the entity.
Polymer entities are expected to have corresponding
ENTITY_POLY and associated entries.
Non-polymer entities are expected to have corresponding
CHEM_COMP and associated entries.
Water entities are not expected to have corresponding
entries in the ENTITY category.
entity.id
The value of attribute id in category entity must uniquely identify a record in the
ENTITY list.
Note that this item need not be a number; it can be any unique
identifier.
entity_keywords
Data items in the ENTITY_KEYWORDS category specify keywords
relevant to the molecular entities. Note that this list of
keywords is separate from the list that is used for the
STRUCT_BIOL data items and is intended to provide only the
information that one would know about the molecular entity *if
one did not know its structure*. Hence polypeptides are simply
polypeptides, not cytokines or beta-alpha-barrels, and
polyribonucleic acids are simply poly-RNA, not transfer-
RNA.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:entity_keywordsCategory>
<PDBx:entity_keywords entity_id="2">
<PDBx:text>natural product, inhibitor, reduced peptide</PDBx:text>
</PDBx:entity_keywords>
</PDBx:entity_keywordsCategory>
0
1
0
1
0
1
0
1
1
entity_keywordsCategory
This property indicates that datablock
has a category element entity_keywords.
entity_keywordsItem
Abstract Datatype property for entity_keywords items.
reference_to_entity_keywords
cross-reference to entity_keywords
entity_keywords.pdbx_ec
Enzyme Commission (EC) number(s)
2.7.7.7
entity_keywords.pdbx_fragment
Entity fragment description(s).
KLENOW FRAGMENT
REPLICASE OPERATOR HAIRPIN
C-TERMINAL DOMAIN
entity_keywords.pdbx_mutation
Entity mutation description(s).
Y31H
DEL(298-323)
entity_keywords.text
Keywords describing this entity.
polypeptide
natural product
polysaccharide
entity_keywords.entity_id
This data item is a pointer to attribute id in category entity in the ENTITY category.
entity_link
Data items in the ENTITY_LINK category give details about
the links between entities.
0
1
1
1
1
1
0
1
0
1
1
entity_linkCategory
This property indicates that datablock
has a category element entity_link.
entity_linkItem
Abstract Datatype property for entity_link items.
reference_to_entity_link
cross-reference to entity_link
entity_link.details
A description of special aspects of a link between
chemical components in the structure.
entity_link.entity_id_1
The entity ID of the first of the two entities joined by the
link.
This data item is a pointer to attribute id in category entity in the ENTITY
category.
entity_link.entity_id_2
The entity ID of the second of the two entities joined by the
link.
This data item is a pointer to attribute id in category entity in the ENTITY
category.
entity_link.entity_seq_num_1
For a polymer entity, the sequence number in the first of
the two entities containing the link.
This data item is a pointer to attribute num in category entity_poly_seq in the
ENTITY_POLY_SEQ category.
entity_link.entity_seq_num_2
For a polymer entity, the sequence number in the second of
the two entities containing the link.
This data item is a pointer to attribute num in category entity_poly_seq in the
ENTITY_POLY_SEQ category.
entity_link.link_id
This data item is a pointer to attribute id in category chem_link in the
CHEM_LINK category.
entity_name_com
Data items in the ENTITY_NAME_COM category record the common name
or names associated with the entity. In some cases, the entity
name may not be the same as the name of the biological structure.
For example, haemoglobin alpha chain would be the entity common
name, not haemoglobin.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:entity_name_comCategory>
<PDBx:entity_name_com entity_id="1">
<PDBx:name>HIV-1 protease monomer</PDBx:name>
</PDBx:entity_name_com>
<PDBx:entity_name_com entity_id="1">
<PDBx:name>HIV-1 PR monomer</PDBx:name>
</PDBx:entity_name_com>
<PDBx:entity_name_com entity_id="2">
<PDBx:name>acetyl-pepstatin</PDBx:name>
</PDBx:entity_name_com>
<PDBx:entity_name_com entity_id="2">
<PDBx:name>acetyl-Ile-Val-Asp-Statine-Ala-Ile-Statine</PDBx:name>
</PDBx:entity_name_com>
<PDBx:entity_name_com entity_id="3">
<PDBx:name>water</PDBx:name>
</PDBx:entity_name_com>
</PDBx:entity_name_comCategory>
0
1
1
entity_name_comCategory
This property indicates that datablock
has a category element entity_name_com.
entity_name_comItem
Abstract Datatype property for entity_name_com items.
reference_to_entity_name_com
cross-reference to entity_name_com
entity_name_com.name
A common name for the entity.
HIV protease monomer
hemoglobin alpha chain
2-fluoro-1,4-dichloro benzene
arbutin
entity_name_com.entity_id
This data item is a pointer to attribute id in category entity in the ENTITY category.
entity_name_sys
Data items in the ENTITY_NAME_SYS category record the systematic
name or names associated with the entity and the system that
was used to construct the systematic name. In some cases, the
entity name may not be the same as the name of the biological
structure.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:entity_name_sysCategory>
<PDBx:entity_name_sys entity_id="1">
<PDBx:name>EC 3.4.23.16</PDBx:name>
</PDBx:entity_name_sys>
<PDBx:entity_name_sys entity_id="2">
<PDBx:name>acetyl-Ile-Val-Asp-Sta-Ala-Ile-Sta</PDBx:name>
</PDBx:entity_name_sys>
<PDBx:entity_name_sys entity_id="3">
<PDBx:name>water</PDBx:name>
</PDBx:entity_name_sys>
</PDBx:entity_name_sysCategory>
0
1
0
1
1
entity_name_sysCategory
This property indicates that datablock
has a category element entity_name_sys.
entity_name_sysItem
Abstract Datatype property for entity_name_sys items.
reference_to_entity_name_sys
cross-reference to entity_name_sys
entity_name_sys.name
The systematic name for the entity.
hydroquinone-beta-D-pyranoside
EC 2.1.1.1
2-fluoro-1,4-dichlorobenzene
entity_name_sys.system
The system used to generate the systematic name of the entity.
Chemical Abstracts conventions
enzyme convention
Sigma catalog
entity_name_sys.entity_id
This data item is a pointer to attribute id in category entity in the ENTITY category.
entity_poly
Data items in the ENTITY_POLY category record details about the
polymer, such as the type of the polymer, the number of
monomers and whether it has nonstandard features.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:entity_polyCategory>
<PDBx:entity_poly entity_id="1">
<PDBx:nstd_chirality>no</PDBx:nstd_chirality>
<PDBx:nstd_linkage>no</PDBx:nstd_linkage>
<PDBx:nstd_monomer>no</PDBx:nstd_monomer>
<PDBx:type>polypeptide(L)</PDBx:type>
<PDBx:type_details></PDBx:type_details>
</PDBx:entity_poly>
</PDBx:entity_polyCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
entity_polyCategory
This property indicates that datablock
has a category element entity_poly.
entity_polyItem
Abstract Datatype property for entity_poly items.
reference_to_entity_poly
cross-reference to entity_poly
no
n
yes
y
A flag to indicate whether the polymer contains at least
one monomer unit with chirality different from that specified in
attribute type in category entity_poly.
no
n
yes
y
A flag to indicate whether the polymer contains at least
one monomer-to-monomer link different from that implied by
attribute type in category entity_poly.
no
n
yes
y
A flag to indicate whether the polymer contains at least
one monomer that is not considered standard.
entity_poly.number_of_monomers
The number of monomers in the polymer.
entity_poly.pdbx_seq_one_letter_code
Chemical sequence expressed as string of one-letter
amino acid codes. Modifications and non-standard
amino acids are coded as X.
A for alanine or adenine
B for ambiguous asparagine/aspartic-acid
R for arginine
N for asparagine
D for aspartic-acid
C for cysteine or cystine or cytosine
Q for glutamine
E for glutamic-acid
Z for ambiguous glutamine/glutamic acid
G for glycine or guanine
H for histidine
I for isoleucine
L for leucine
K for lysine
M for methionine
F for phenylalanine
P for proline
S for serine
T for threonine or thymine
W for tryptophan
Y for tyrosine
V for valine
U for uracil
O for water
X for other
entity_poly.pdbx_seq_one_letter_code_can
Cannonical chemical sequence expressed as string of
one-letter amino acid codes. Modifications are coded
as the parent amino acid where possible.
A for alanine or adenine
B for ambiguous asparagine/aspartic-acid
R for arginine
N for asparagine
D for aspartic-acid
C for cysteine or cystine or cytosine
Q for glutamine
E for glutamic-acid
Z for ambiguous glutamine/glutamic acid
G for glycine or guanine
H for histidine
I for isoleucine
L for leucine
K for lysine
M for methionine
F for phenylalanine
P for proline
S for serine
T for threonine or thymine
W for tryptophan
Y for tyrosine
V for valine
U for uracil
MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD
entity_poly.pdbx_strand_id
The PDB strand/chain id(s) corresponding to this polymer entity.
A
B
A,B,C
entity_poly.pdbx_target_identifier
The sequence's target identifier registered at target database.
356560
polypeptide(D)
polypeptide(L)
polydeoxyribonucleotide
polyribonucleotide
polysaccharide(D)
polysaccharide(L)
polydeoxyribonucleotide/polyribonucleotide hybrid
cyclic-pseudo-peptide
other
The type of the polymer.
entity_poly.type_details
A description of special aspects of the polymer type.
monomer Ala 16 is a D-amino acid
the oligomer contains alternating RNA and DNA units
entity_poly.entity_id
This data item is a pointer to attribute id in category entity in the ENTITY category.
entity_poly_seq
Data items in the ENTITY_POLY_SEQ category specify the sequence
of monomers in a polymer. Allowance is made for the possibility
of microheterogeneity in a sample by allowing a given sequence
number to be correlated with more than one monomer ID. The
corresponding ATOM_SITE entries should reflect this
heterogeneity.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:entity_poly_seqCategory>
<PDBx:entity_poly_seq entity_id="1" mon_id="PRO" num="1"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="GLN" num="2"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="ILE" num="3"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="THR" num="4"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="LEU" num="5"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="TRP" num="6"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="GLN" num="7"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="ARG" num="8"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="PRO" num="9"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="LEU" num="10"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="VAL" num="11"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="THR" num="12"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="ILE" num="13"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="LYS" num="14"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="ILE" num="15"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="GLY" num="16"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="GLY" num="17"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="GLN" num="18"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="LEU" num="19"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="LYS" num="20"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="GLU" num="21"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="ALA" num="22"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="LEU" num="23"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="LEU" num="24"></PDBx:entity_poly_seq>
<PDBx:entity_poly_seq entity_id="1" mon_id="ASP" num="25"></PDBx:entity_poly_seq>
</PDBx:entity_poly_seqCategory>
0
1
1
1
1
entity_poly_seqCategory
This property indicates that datablock
has a category element entity_poly_seq.
entity_poly_seqItem
Abstract Datatype property for entity_poly_seq items.
reference_to_entity_poly_seq
cross-reference to entity_poly_seq
no
n
yes
y
A flag to indicate whether this monomer in the polymer is
heterogeneous in sequence. This would be rare.
entity_poly_seq.entity_id
This data item is a pointer to attribute id in category entity in the ENTITY category.
entity_poly_seq.mon_id
This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP
category.
entity_poly_seq.num
The value of attribute num in category entity_poly_seq must uniquely and sequentially
identify a record in the ENTITY_POLY_SEQ list.
Note that this item must be a number and that the sequence
numbers must progress in increasing numerical order.
entity_src_gen
Data items in the ENTITY_SRC_GEN category record details of
the source from which the entity was obtained in cases
where the source was genetically manipulated. The
following are treated separately: items pertaining to the tissue
from which the gene was obtained, items pertaining to the host
organism for gene expression and items pertaining to the actual
producing organism (plasmid).
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:entity_src_genCategory>
<PDBx:entity_src_gen entity_id="1">
<PDBx:gene_src_common_name>HIV-1</PDBx:gene_src_common_name>
<PDBx:gene_src_genus xsi:nil="true" />
<PDBx:gene_src_species xsi:nil="true" />
<PDBx:gene_src_strain>NY-5</PDBx:gene_src_strain>
<PDBx:host_org_common_name>bacteria</PDBx:host_org_common_name>
<PDBx:host_org_genus>Escherichia</PDBx:host_org_genus>
<PDBx:host_org_species>coli</PDBx:host_org_species>
<PDBx:plasmid_name>pB322</PDBx:plasmid_name>
</PDBx:entity_src_gen>
</PDBx:entity_src_genCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
entity_src_genCategory
This property indicates that datablock
has a category element entity_src_gen.
entity_src_genItem
Abstract Datatype property for entity_src_gen items.
reference_to_entity_src_gen
cross-reference to entity_src_gen
entity_src_gen.expression_system_id
A unique identifier for the expression system. This
should be extracted from a local list of expression
systems.
entity_src_gen.gene_src_common_name
The common name of the natural organism from which the gene was
obtained.
man
yeast
bacteria
entity_src_gen.gene_src_details
A description of special aspects of the natural organism from
which the gene was obtained.
entity_src_gen.gene_src_dev_stage
A string to indicate the life-cycle or cell development
cycle in which the gene is expressed and the mature
protein is active.
entity_src_gen.gene_src_genus
The genus of the natural organism from which the gene was
obtained.
Homo
Saccharomyces
Escherichia
entity_src_gen.gene_src_species
The species of the natural organism from which the gene was
obtained.
sapiens
cerevisiae
coli
entity_src_gen.gene_src_strain
The strain of the natural organism from which the gene was
obtained, if relevant.
DH5a
BMH 71-18
entity_src_gen.gene_src_tissue
The tissue of the natural organism from which the gene was
obtained.
heart
liver
eye lens
entity_src_gen.gene_src_tissue_fraction
The subcellular fraction of the tissue of the natural organism
from which the gene was obtained.
mitochondria
nucleus
membrane
entity_src_gen.host_org_common_name
The common name of the organism that served as host for the
production of the entity. Where full details of the protein
production are available it would be expected that this item
be derived from attribute host_org_common_name
in category entity_src_gen_express or via attribute host_org_tax_id in category entity_src_gen_express
yeast
bacteria
entity_src_gen.host_org_details
A description of special aspects of the organism that served as
host for the production of the entity. Where full details of
the protein production are available it would be expected that
this item would derived from attribute host_org_details in category entity_src_gen_express
entity_src_gen.host_org_genus
The genus of the organism that served as host for the production
of the entity.
Saccharomyces
Escherichia
entity_src_gen.host_org_species
The species of the organism that served as host for the
production of the entity.
cerevisiae
coli
entity_src_gen.host_org_strain
The strain of the organism in which the entity was expressed.
Where full details of the protein production are available
it would be expected that this item be derived from
attribute host_org_strain in category entity_src_gen_express or via
attribute host_org_tax_id in category entity_src_gen_express
DH5a
BMH 71-18
entity_src_gen.pdbx_description
Information on the source which is not given elsewhere.
entity_src_gen.pdbx_gene_src_atcc
American Type Culture Collection tissue culture number.
6051
entity_src_gen.pdbx_gene_src_cell
Cell type.
ENDOTHELIAL
entity_src_gen.pdbx_gene_src_cell_line
The specific line of cells.
HELA CELLS
entity_src_gen.pdbx_gene_src_cellular_location
Identifies the location inside (or outside) the cell.
CYTOPLASM
NUCLEUS
entity_src_gen.pdbx_gene_src_fragment
A domain or fragment of the molecule.
CYTOPLASM
NUCLEUS
entity_src_gen.pdbx_gene_src_gene
Identifies the gene.
entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id
NCBI Taxonomy identifier for the gene source organism.
Reference:
Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD,
Tatusova TA, Rapp BA (2000). Database resources of the National
Center for Biotechnology Information. Nucleic Acids Res 2000 Jan
1;28(1):10-4
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA,
Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.
entity_src_gen.pdbx_gene_src_organ
Organized group of tissues that carries on a specialized function.
KIDNEY
LIVER
PANCREAS
entity_src_gen.pdbx_gene_src_organelle
Organized structure within cell.
MITOCHONDRIA
entity_src_gen.pdbx_gene_src_plasmid
The source plasmid.
entity_src_gen.pdbx_gene_src_plasmid_name
The source plasmid.
entity_src_gen.pdbx_gene_src_scientific_name
Scientific name of the organism.
ESCHERICHIA COLI
HOMO SAPIENS
SACCHAROMYCES CEREVISIAE
entity_src_gen.pdbx_gene_src_variant
Identifies the variant.
DELTAH1DELTATRP
entity_src_gen.pdbx_host_org_atcc
Americal Tissue Culture Collection of the expression system. Where
full details of the protein production are available it would
be expected that this item would be derived from
attribute host_org_culture_collection in category entity_src_gen_express
entity_src_gen.pdbx_host_org_cell
Cell type from which the gene is derived. Where
entity.target_id is provided this should be derived from
details of the target.
ENDOTHELIAL
entity_src_gen.pdbx_host_org_cell_line
A specific line of cells used as the expression system. Where
full details of the protein production are available it would
be expected that this item would be derived from
entity_src_gen_express.host_org_cell_line
HELA
entity_src_gen.pdbx_host_org_cellular_location
Identifies the location inside (or outside) the cell which
expressed the molecule.
CYTOPLASM
NUCLEUS
entity_src_gen.pdbx_host_org_culture_collection
Culture collection of the expression system. Where
full details of the protein production are available it would
be expected that this item would be derived somehwere, but
exactly where is not clear.
entity_src_gen.pdbx_host_org_gene
Specific gene which expressed the molecule.
HIV-1 POL
GLNS7
U1A (2-98, Y31H, Q36R)
entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
NCBI Taxonomy identifier for the expression system organism.
Reference:
Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD,
Tatusova TA, Rapp BA (2000). Database resources of the National
Center for Biotechnology Information. Nucleic Acids Res 2000 Jan
1;28(1):10-4
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA,
Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.
entity_src_gen.pdbx_host_org_organ
Specific organ which expressed the molecule.
KIDNEY
entity_src_gen.pdbx_host_org_organelle
Specific organelle which expressed the molecule.
MITOCHONDRIA
entity_src_gen.pdbx_host_org_scientific_name
The scientific name of the organism that served as host for the
production of the entity. Where full details of the protein
production are available it would be expected that this item
would be derived from attribute host_org_scientific_name
in category entity_src_gen_express or via attribute host_org_tax_id in category entity_src_gen_express
ESCHERICHIA COLI
SACCHAROMYCES CEREVISIAE
entity_src_gen.pdbx_host_org_strain
The strain of the organism in which the entity was
expressed.
AR120
entity_src_gen.pdbx_host_org_tissue
The specific tissue which expressed the molecule. Where full details
of the protein production are available it would be expected that this
item would be derived from attribute host_org_tissue in category entity_src_gen_express
heart
liver
eye lens
entity_src_gen.pdbx_host_org_tissue_fraction
The fraction of the tissue which expressed the
molecule.
mitochondria
nucleus
membrane
entity_src_gen.pdbx_host_org_variant
Variant of the organism used as the expression system. Where
full details of the protein production are available it would
be expected that this item be derived from
entity_src_gen_express.host_org_variant or via
attribute host_org_tax_id in category entity_src_gen_express
TRP-LAC
LAMBDA DE3
entity_src_gen.pdbx_host_org_vector
Identifies the vector used. Where full details of the protein
production are available it would be expected that this item
would be derived from attribute vector_name in category entity_src_gen_clone.
PBIT36
PET15B
PUC18
entity_src_gen.pdbx_host_org_vector_type
Identifies the type of vector used (plasmid, virus, or cosmid).
Where full details of the protein production are available it
would be expected that this item would be derived from
attribute vector_type in category entity_src_gen_express.
COSMID
PLASMID
entity_src_gen.plasmid_details
A description of special aspects of the plasmid that produced the
entity in the host organism. Where full details of the protein
production are available it would be expected that this item
would be derived from attribute details in category pdbx_construct of the construct
pointed to from attribute plasmid_id in category entity_src_gen_express.
entity_src_gen.plasmid_name
The name of the plasmid that produced the entity in the host
organism. Where full details of the protein production are available
it would be expected that this item would be derived from
attribute name in category pdbx_construct of the construct pointed to from
attribute plasmid_id in category entity_src_gen_express.
pET3C
pT123sab
entity_src_gen.start_construct_id
A pointer to attribute id in category pdbx_construct in the PDBX_CONSTRUCT category.
The indentified sequence is the initial construct.
entity_src_gen.entity_id
This data item is a pointer to attribute id in category entity in the ENTITY category.
entity_src_nat
Data items in the ENTITY_SRC_NAT category record details of
the source from which the entity was obtained in cases
where the entity was isolated directly from a natural tissue.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:entity_src_natCategory>
<PDBx:entity_src_nat entity_id="2">
<PDBx:common_name>bacteria</PDBx:common_name>
<PDBx:details> Acetyl-pepstatin was isolated by Dr. K. Oda, Osaka
Prefecture University, and provided to us by Dr. Ben
Dunn, University of Florida, and Dr. J. Kay, University
of Wales.</PDBx:details>
<PDBx:genus>Actinomycetes</PDBx:genus>
<PDBx:species xsi:nil="true" />
</PDBx:entity_src_nat>
</PDBx:entity_src_natCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
entity_src_natCategory
This property indicates that datablock
has a category element entity_src_nat.
entity_src_natItem
Abstract Datatype property for entity_src_nat items.
reference_to_entity_src_nat
cross-reference to entity_src_nat
entity_src_nat.common_name
The common name of the organism from which the entity
was isolated.
man
yeast
bacteria
entity_src_nat.details
A description of special aspects of the organism from which the
entity was isolated.
entity_src_nat.genus
The genus of the organism from which the entity was isolated.
Homo
Saccharomyces
Escherichia
entity_src_nat.pdbx_atcc
Americal Tissue Culture Collection number.
6051
entity_src_nat.pdbx_cell
A particular cell type.
BHK-21
entity_src_nat.pdbx_cell_line
The specific line of cells.
HELA
entity_src_nat.pdbx_cellular_location
Identifies the location inside (or outside) the cell.
entity_src_nat.pdbx_fragment
A domain or fragment of the molecule.
entity_src_nat.pdbx_ncbi_taxonomy_id
NCBI Taxonomy identifier for the source organism.
Reference:
Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD,
Tatusova TA, Rapp BA (2000). Database resources of the National
Center for Biotechnology Information. Nucleic Acids Res 2000 Jan
1;28(1):10-4
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA,
Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.
entity_src_nat.pdbx_organ
Organized group of tissues that carries on a specialized function.
KIDNEY
entity_src_nat.pdbx_organelle
Organized structure within cell.
MITOCHONDRIA
entity_src_nat.pdbx_organism_scientific
Scientific name of the organism of the natural source.
BOS TAURUS
SUS SCROFA
ASPERGILLUS ORYZAE
entity_src_nat.pdbx_plasmid_details
Details about the plasmid.
PLC28 DERIVATIVE
entity_src_nat.pdbx_plasmid_name
The plasmid containing the gene.
pB322
entity_src_nat.pdbx_secretion
Identifies the secretion from which the molecule was isolated.
saliva
urine
venom
entity_src_nat.pdbx_variant
Identifies the variant.
entity_src_nat.species
The species of the organism from which the entity was isolated.
sapiens
cerevisiae
coli
entity_src_nat.strain
The strain of the organism from which the entity was isolated.
DH5a
BMH 71-18
entity_src_nat.tissue
The tissue of the organism from which the entity was isolated.
heart
liver
eye lens
entity_src_nat.tissue_fraction
The subcellular fraction of the tissue of the organism from
which the entity was isolated.
mitochondria
nucleus
membrane
entity_src_nat.entity_id
This data item is a pointer to attribute id in category entity in the ENTITY category.
entry
There is only one item in the ENTRY category, attribute id in category entry. This
data item gives a name to this entry and is indirectly a key to
the categories (such as CELL, GEOM, EXPTL) that describe
information pertinent to the entire data block.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:entryCategory>
<PDBx:entry id="5HVP"></PDBx:entry>
</PDBx:entryCategory>
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<PDBx:entryCategory>
<PDBx:entry id="TOZ"></PDBx:entry>
</PDBx:entryCategory>
0
1
1
entryCategory
This property indicates that datablock
has a category element entry.
entryItem
Abstract Datatype property for entry items.
reference_to_entry
cross-reference to entry
entry.pdbx_DOI
Document Object Identifier (DOI) for this entry registered
with http://crossref.org.
entry.id
The value of attribute id in category entry identifies the data block.
Note that this item need not be a number; it can be any unique
identifier.
entry_link
Data items in the ENTRY_LINK category record the
relationships between the current data block
identified by attribute id in category entry and other data blocks
within the current file which may be referenced
in the current data block.
Example 1 - example file for the one-dimensional incommensurately
modulated structure of K~2~SeO~4~.
<PDBx:entry_linkCategory>
<PDBx:entry_link entry_id="KSE_TEXT" id="KSE_COM">
<PDBx:details>experimental data common to ref./mod. structures</PDBx:details>
</PDBx:entry_link>
<PDBx:entry_link entry_id="KSE_TEXT" id="KSE_REF">
<PDBx:details>reference structure</PDBx:details>
</PDBx:entry_link>
<PDBx:entry_link entry_id="KSE_TEXT" id="KSE_MOD">
<PDBx:details>modulated structure</PDBx:details>
</PDBx:entry_link>
</PDBx:entry_linkCategory>
0
1
1
1
entry_linkCategory
This property indicates that datablock
has a category element entry_link.
entry_linkItem
Abstract Datatype property for entry_link items.
reference_to_entry_link
cross-reference to entry_link
entry_link.details
A description of the relationship between the data blocks
identified by _entry_link.id and _entry_link.entry_id.
entry_link.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
entry_link.id
The value of attribute id in category entry_link identifies a data block
related to the current data block.
exptl
Data items in the EXPTL category record details about the
experimental work prior to the intensity measurements and
details about the absorption-correction technique employed.
Example 1 - based on laboratory records for Yb(S-C5H4N)2(THF)4.
<PDBx:exptlCategory>
<PDBx:exptl entry_id="datablock1" method="single-crystal x-ray diffraction">
<PDBx:absorpt_coefficient_mu>1.22</PDBx:absorpt_coefficient_mu>
<PDBx:absorpt_correction_T_max>0.896</PDBx:absorpt_correction_T_max>
<PDBx:absorpt_correction_T_min>0.802</PDBx:absorpt_correction_T_min>
<PDBx:absorpt_correction_type>integration</PDBx:absorpt_correction_type>
<PDBx:absorpt_process_details> Gaussian grid method from SHELX76
Sheldrick, G. M., "SHELX-76: structure determination and
refinement program", Cambridge University, UK, 1976</PDBx:absorpt_process_details>
<PDBx:crystals_number>1</PDBx:crystals_number>
<PDBx:details> Enraf-Nonius LT2 liquid nitrogen variable-temperature
device used</PDBx:details>
<PDBx:method_details> graphite monochromatized Cu K(alpha) fixed tube and
Enraf-Nonius CAD4 diffractometer used</PDBx:method_details>
</PDBx:exptl>
</PDBx:exptlCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
exptlCategory
This property indicates that datablock
has a category element exptl.
exptlItem
Abstract Datatype property for exptl items.
reference_to_exptl
cross-reference to exptl
exptl.absorpt_coefficient_mu
The absorption coefficient mu in reciprocal millimetres
calculated from the atomic content of the cell, the density and
the radiation wavelength.
exptl.absorpt_correction_T_max
The maximum transmission factor for the crystal and radiation.
The maximum and minimum transmission factors are also referred
to as the absorption correction
A or 1/A*.
exptl.absorpt_correction_T_min
The minimum transmission factor for the crystal and radiation.
The maximum and minimum transmission factors are also referred
to as the absorption correction
A or 1/A*.
analytical
cylinder
empirical
gaussian
integration
multi-scan
none
numerical
psi-scan
refdelf
sphere
The absorption correction type and method. The value
'empirical' should NOT be used unless more detailed
information is not available.
exptl.absorpt_process_details
Description of the absorption process applied to the
intensities. A literature reference should be supplied for
psi-scan techniques.
Tompa analytical
exptl.crystals_number
The total number of crystals used in the measurement of
intensities.
exptl.details
Any special information about the experimental work prior to the
intensity measurement. See also attribute preparation in category exptl_crystal.
exptl.method_details
A description of special aspects of the experimental method.
29 structures
minimized average structure
exptl.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
X-RAY DIFFRACTION
NEUTRON DIFFRACTION
FIBER DIFFRACTION
ELECTRON CRYSTALLOGRAPHY
ELECTRON MICROSCOPY
SOLUTION NMR
SOLID-STATE NMR
SOLUTION SCATTERING
POWDER DIFFRACTION
INFRARED SPECTROSCOPY
The method used in the experiment.
X-RAY DIFFRACTION
NEUTRON DIFFRACTION
FIBER DIFFRACTION
ELECTRON CRYSTALLOGRAPHY
ELECTRON MICROSCOPY
SOLUTION NMR
SOLID-STATE NMR
SOLUTION SCATTERING
POWDER DIFFRACTION
exptl_crystal
Data items in the EXPTL_CRYSTAL category record the results of
experimental measurements on the crystal or crystals used,
such as shape, size or density.
Example 1 - based on laboratory records for Yb(S-C5H4N)2(THF)4.
<PDBx:exptl_crystalCategory>
<PDBx:exptl_crystal id="xst2l">
<PDBx:F_000>202</PDBx:F_000>
<PDBx:colour>pale yellow</PDBx:colour>
<PDBx:density_Matthews>1.01</PDBx:density_Matthews>
<PDBx:density_diffrn>1.113</PDBx:density_diffrn>
<PDBx:density_meas>1.11</PDBx:density_meas>
<PDBx:density_meas_temp>294.5</PDBx:density_meas_temp>
<PDBx:density_method>neutral buoyancy</PDBx:density_method>
<PDBx:density_percent_sol>0.15</PDBx:density_percent_sol>
<PDBx:description>hexagonal rod, uncut</PDBx:description>
<PDBx:preparation> hanging drop, crystal soaked in 10% ethylene glycol for
10 h, then placed in nylon loop at data collection time</PDBx:preparation>
<PDBx:size_max>0.30</PDBx:size_max>
<PDBx:size_mid>0.20</PDBx:size_mid>
<PDBx:size_min>0.05</PDBx:size_min>
<PDBx:size_rad>0.025</PDBx:size_rad>
</PDBx:exptl_crystal>
</PDBx:exptl_crystalCategory>
Example 2 - using separate items to define upper and lower
limits for a value.
<PDBx:exptl_crystalCategory>
<PDBx:exptl_crystal id="xst2l">
<PDBx:density_meas_gt>2.5</PDBx:density_meas_gt>
<PDBx:density_meas_lt>5.0</PDBx:density_meas_lt>
</PDBx:exptl_crystal>
</PDBx:exptl_crystalCategory>
Example 3 - here the density was measured at some
unspecified temperature below room temperature.
<PDBx:exptl_crystalCategory>
<PDBx:exptl_crystal id="xst2l">
<PDBx:density_meas_temp_lt>300</PDBx:density_meas_temp_lt>
</PDBx:exptl_crystal>
</PDBx:exptl_crystalCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
exptl_crystalCategory
This property indicates that datablock
has a category element exptl_crystal.
exptl_crystalItem
Abstract Datatype property for exptl_crystal items.
reference_to_exptl_crystal
cross-reference to exptl_crystal
exptl_crystal.F_000
The effective number of electrons in the crystal unit cell
contributing to F(000). This may contain dispersion contributions
and is calculated as
F(000) = [ sum (f~r~^2^ + f~i~^2^) ]^1/2^
f~r~ = real part of the scattering factors at theta = 0 degree
f~i~ = imaginary part of the scattering factors at
theta = 0 degree
the sum is taken over each atom in the unit cell
exptl_crystal.colour
The colour of the crystal.
dark green
metallic
dull
clear
The enumeration list of standardized names developed for the
International Centre for Diffraction Data.
The colour of a crystal is given by the combination of
attribute colour_modifier in category exptl_crystal with
attribute colour_primary in category exptl_crystal, as in 'dark-green' or
'bluish-violet', if necessary combined with
attribute colour_lustre in category exptl_crystal, as in 'metallic-green'.
light
dark
whitish
blackish
grayish
brownish
reddish
pinkish
orangish
yellowish
greenish
bluish
The enumeration list of standardized names developed for the
International Centre for Diffraction Data.
The colour of a crystal is given by the combination of
attribute colour_modifier in category exptl_crystal with
attribute colour_primary in category exptl_crystal, as in 'dark-green' or
'bluish-violet', if necessary combined with
attribute colour_lustre in category exptl_crystal, as in 'metallic-green'.
colourless
white
black
gray
brown
red
pink
orange
yellow
green
blue
violet
The enumeration list of standardized names developed for the
International Centre for Diffraction Data.
The colour of a crystal is given by the combination of
attribute colour_modifier in category exptl_crystal with
attribute colour_primary in category exptl_crystal, as in 'dark-green' or
'bluish-violet', if necessary combined with
attribute colour_lustre in category exptl_crystal, as in 'metallic-green'.
exptl_crystal.density_Matthews
The density of the crystal, expressed as the ratio of the
volume of the asymmetric unit to the molecular mass of a
monomer of the structure, in units of angstroms^3^ per dalton.
Ref: Matthews, B. W. (1968). J. Mol. Biol. 33, 491-497.
exptl_crystal.density_diffrn
Density values calculated from the crystal cell and contents. The
units are megagrams per cubic metre (grams per cubic centimetre).
exptl_crystal.density_meas
Density values measured using standard chemical and physical
methods. The units are megagrams per cubic metre (grams per
cubic centimetre).
exptl_crystal.density_meas_esd
The estimated standard deviation of attribute density_meas in category exptl_crystal.
exptl_crystal.density_meas_gt
The value above which the density measured using standard
chemical and physical methods lies. The units are megagrams
per cubic metre (grams per cubic centimetre).
_exptl_crystal.density_meas_gt and _exptl_crystal.density_meas_lt
should not be used to report new experimental work, for which
attribute density_meas in category exptl_crystal should be used. These items are
intended for use in reporting information in existing databases
and archives which would be misleading if reported under
attribute density_meas in category exptl_crystal.
lower limit for the density (only the range
within which the density lies was given in the
original paper)
2.5
exptl_crystal.density_meas_lt
The value below which the density measured using standard
chemical and physical methods lies. The units are megagrams
per cubic metre (grams per cubic centimetre).
_exptl_crystal.density_meas_gt and _exptl_crystal.density_meas_lt
should not be used to report new experimental work, for which
attribute density_meas in category exptl_crystal should be used. These items are
intended for use in reporting information in existing databases
and archives which would be misleading if reported under
attribute density_meas in category exptl_crystal.
specimen floats in water
1.0
upper limit for the density (only the range
within which the density lies was given in the
original paper)
5.0
exptl_crystal.density_meas_temp
Temperature in kelvins at which attribute density_meas
in category exptl_crystal was determined.
exptl_crystal.density_meas_temp_esd
The estimated standard deviation of
attribute density_meas_temp in category exptl_crystal.
exptl_crystal.density_meas_temp_gt
Temperature in kelvins above which attribute density_meas
in category exptl_crystal was determined. attribute density_meas_temp_gt in category exptl_crystal and
attribute density_meas_temp_lt in category exptl_crystal should not be used for
reporting new work, for which the correct temperature of
measurement should be given. These items are intended for
use in reporting information stored in databases or archives
which would be misleading if reported under
attribute density_meas_temp in category exptl_crystal.
exptl_crystal.density_meas_temp_lt
Temperature in kelvins below which attribute density_meas
in category exptl_crystal was determined. attribute density_meas_temp_gt in category exptl_crystal and
attribute density_meas_temp_lt in category exptl_crystal should not be used for
reporting new work, for which the correct temperature of
measurement should be given. These items are intended for
use in reporting information stored in databases or archives
which would be misleading if reported under
attribute density_meas_temp in category exptl_crystal.
The density was measured at some unspecified
temperature below room temperature.
300
exptl_crystal.density_method
The method used to measure attribute density_meas in category exptl_crystal.
exptl_crystal.density_percent_sol
Density value P calculated from the crystal cell and contents,
expressed as per cent solvent.
P = 1 - (1.23 N MMass) / V
N = the number of molecules in the unit cell
MMass = the molecular mass of each molecule (gm/mole)
V = the volume of the unit cell (A^3^)
1.23 = a conversion factor evaluated as:
(0.74 cm^3^/g) (10^24^ A^3^/cm^3^)
--------------------------------------
(6.02*10^23^) molecules/mole
where 0.74 is an assumed value for the partial specific
volume of the molecule
exptl_crystal.description
A description of the quality and habit of the crystal.
The crystal dimensions should not normally be reported here;
use instead the specific items in the EXPTL_CRYSTAL category
relating to size for the gross dimensions of the crystal and
data items in the EXPTL_CRYSTAL_FACE category to describe the
relationship between individual faces.
exptl_crystal.pdbx_crystal_image_format
The image format for the file containing the image of crystal specified
as an RFC2045/RFC2046 mime type.
jpeg
gif
tiff
exptl_crystal.pdbx_crystal_image_url
The URL for an a file containing the image of crystal.
exptl_crystal.pdbx_mosaicity
The of the distribution of mis-orientation angles specified in degrees
of all the unit cells in the crystal. Lower mosaicity indicates better
ordered crystals.
exptl_crystal.pdbx_mosaicity_esd
The uncertainty in the mosaicity estimate for the crystal.
exptl_crystal.preparation
Details of crystal growth and preparation of the crystal (e.g.
mounting) prior to the intensity measurements.
mounted in an argon-filled quartz capillary
exptl_crystal.size_max
The maximum dimension of the crystal. This item may appear in a
list with attribute id in category exptl_crystal if multiple crystals are used in the
experiment.
exptl_crystal.size_mid
The medial dimension of the crystal. This item may appear in a
list with attribute id in category exptl_crystal if multiple crystals are used in the
experiment.
exptl_crystal.size_min
The minimum dimension of the crystal. This item may appear in a
list with attribute id in category exptl_crystal if multiple crystals are used in the
experiment.
exptl_crystal.size_rad
The radius of the crystal, if the crystal is a sphere or a
cylinder. This item may appear in a list with attribute id
in category exptl_crystal if multiple crystals are used in the experiment.
exptl_crystal.id
The value of attribute id in category exptl_crystal must uniquely identify a record in
the EXPTL_CRYSTAL list.
Note that this item need not be a number; it can be any unique
identifier.
exptl_crystal_face
Data items in the EXPTL_CRYSTAL_FACE category record details
of the crystal faces.
Example 1 - based on laboratory records for Yb(S-C5H4N)2(THF)4
for the 100 face of crystal xstl1.
<PDBx:exptl_crystal_faceCategory>
<PDBx:exptl_crystal_face crystal_id="xstl1" index_h="1" index_k="0" index_l="0">
<PDBx:diffr_chi>42.56</PDBx:diffr_chi>
<PDBx:diffr_kappa>30.23</PDBx:diffr_kappa>
<PDBx:diffr_phi>-125.56</PDBx:diffr_phi>
<PDBx:diffr_psi>-0.34</PDBx:diffr_psi>
<PDBx:perp_dist>0.025</PDBx:perp_dist>
</PDBx:exptl_crystal_face>
</PDBx:exptl_crystal_faceCategory>
0
1
0
1
0
1
0
1
0
1
1
1
1
1
exptl_crystal_faceCategory
This property indicates that datablock
has a category element exptl_crystal_face.
exptl_crystal_faceItem
Abstract Datatype property for exptl_crystal_face items.
reference_to_exptl_crystal_face
cross-reference to exptl_crystal_face
exptl_crystal_face.diffr_chi
The chi diffractometer setting angle in degrees for a specific
crystal face associated with attribute perp_dist in category exptl_crystal_face.
exptl_crystal_face.diffr_kappa
The kappa diffractometer setting angle in degrees for a specific
crystal face associated with attribute perp_dist in category exptl_crystal_face.
exptl_crystal_face.diffr_phi
The phi diffractometer setting angle in degrees for a specific
crystal face associated with attribute perp_dist in category exptl_crystal_face.
exptl_crystal_face.diffr_psi
The psi diffractometer setting angle in degrees for a specific
crystal face associated with attribute perp_dist in category exptl_crystal_face.
exptl_crystal_face.perp_dist
The perpendicular distance in millimetres from the face to the
centre of rotation of the crystal.
exptl_crystal_face.crystal_id
This data item is a pointer to attribute id in category exptl_crystal in the
EXPTL_CRYSTAL category.
exptl_crystal_face.index_h
Miller index h of the crystal face associated with the value
attribute perp_dist in category exptl_crystal_face.
exptl_crystal_face.index_k
Miller index k of the crystal face associated with the value
attribute perp_dist in category exptl_crystal_face.
exptl_crystal_face.index_l
Miller index l of the crystal face associated with the value
attribute perp_dist in category exptl_crystal_face.
exptl_crystal_grow
Data items in the EXPTL_CRYSTAL_GROW category record details
about the conditions and methods used to grow the crystal.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:exptl_crystal_growCategory>
<PDBx:exptl_crystal_grow crystal_id="1">
<PDBx:apparatus>Linbro plates</PDBx:apparatus>
<PDBx:atmosphere>room air</PDBx:atmosphere>
<PDBx:method>hanging drop</PDBx:method>
<PDBx:pH>4.7</PDBx:pH>
<PDBx:temp>18.</PDBx:temp>
<PDBx:time>approximately 2 days</PDBx:time>
</PDBx:exptl_crystal_grow>
</PDBx:exptl_crystal_growCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
exptl_crystal_growCategory
This property indicates that datablock
has a category element exptl_crystal_grow.
exptl_crystal_growItem
Abstract Datatype property for exptl_crystal_grow items.
reference_to_exptl_crystal_grow
cross-reference to exptl_crystal_grow
exptl_crystal_grow.apparatus
The physical apparatus in which the crystal was grown.
Linbro plate
sandwich box
ACA plates
exptl_crystal_grow.atmosphere
The nature of the gas or gas mixture in which the crystal was
grown.
room air
nitrogen
argon
exptl_crystal_grow.details
A description of special aspects of the crystal growth.
Solution 2 was prepared as a well solution and
mixed. A droplet containing 2 \ml of solution
1 was delivered onto a cover slip; 2 \ml of
solution 2 was added to the droplet without
mixing.
Crystal plates were originally stored at room
temperature for 1 week but no nucleation
occurred. They were then transferred to 4
degrees C, at which temperature well formed
single crystals grew in 2 days.
The dependence on pH for successful crystal
growth is very sharp. At pH 7.4 only showers
of tiny crystals grew, at pH 7.5 well formed
single crystals grew, at pH 7.6 no
crystallization occurred at all.
exptl_crystal_grow.method
The method used to grow the crystals.
batch precipitation
batch dialysis
hanging drop vapor diffusion
sitting drop vapor diffusion
exptl_crystal_grow.method_ref
A literature reference that describes the method used to grow
the crystals.
McPherson et al., 1988
exptl_crystal_grow.pH
The pH at which the crystal was grown. If more than one pH was
employed during the crystallization process, the final pH should
be noted here and the protocol involving multiple pH values
should be described in attribute details in category exptl_crystal_grow.
7.4
7.6
4.3
exptl_crystal_grow.pdbx_details
Text description of crystal grow procedure.
PEG 4000, potassium phosphate, magnesium chloride, cacodylate
exptl_crystal_grow.pdbx_pH_range
The range of pH values at which the crystal was grown. Used when
a point estimate of pH is not appropriate.
5.6 - 6.4
exptl_crystal_grow.pressure
The ambient pressure in kilopascals at which the crystal was
grown.
exptl_crystal_grow.pressure_esd
The standard uncertainty (estimated standard deviation)
of attribute pressure in category exptl_crystal_grow.
exptl_crystal_grow.seeding
A description of the protocol used for seeding the crystal
growth.
macroseeding
Microcrystals were introduced from a previous
crystal growth experiment by transfer with a
human hair.
exptl_crystal_grow.seeding_ref
A literature reference that describes the protocol used to seed
the crystal.
Stura et al., 1989
exptl_crystal_grow.temp
The temperature in kelvins at which the crystal was grown.
If more than one temperature was employed during the
crystallization process, the final temperature should be noted
here and the protocol involving multiple temperatures should be
described in attribute details in category exptl_crystal_grow.
exptl_crystal_grow.temp_details
A description of special aspects of temperature control during
crystal growth.
exptl_crystal_grow.temp_esd
The standard uncertainty (estimated standard deviation)
of attribute temp in category exptl_crystal_grow.
exptl_crystal_grow.time
The approximate time that the crystal took to grow to the size
used for data collection.
overnight
2-4 days
6 months
exptl_crystal_grow.crystal_id
This data item is a pointer to attribute id in category exptl_crystal in the
EXPTL_CRYSTAL category.
exptl_crystal_grow_comp
Data items in the EXPTL_CRYSTAL_GROW_COMP category record
details about the components of the solutions that were 'mixed'
(by whatever means) to produce the crystal.
In general, solution 1 is the solution that contains the
molecule to be crystallized and solution 2 is the solution
that contains the precipitant. However, the number of solutions
required to describe the crystallization protocol is not limited
to 2.
Details of the crystallization protocol should be given in
attribute details in category exptl_crystal_grow_comp using the solutions
described in EXPTL_CRYSTAL_GROW_COMP.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:exptl_crystal_grow_compCategory>
<PDBx:exptl_crystal_grow_comp crystal_id="1" id="1">
<PDBx:conc>6 mg/ml</PDBx:conc>
<PDBx:details> The protein solution was in a buffer containing 25 mM NaCl,
100 mM NaMES/ MES buffer, pH 7.5, 3 mM NaAzide</PDBx:details>
<PDBx:name>HIV-1 protease</PDBx:name>
<PDBx:sol_id>1</PDBx:sol_id>
<PDBx:volume>0.002 ml</PDBx:volume>
</PDBx:exptl_crystal_grow_comp>
<PDBx:exptl_crystal_grow_comp crystal_id="1" id="2">
<PDBx:conc>4 M</PDBx:conc>
<PDBx:details>in 3 mM NaAzide</PDBx:details>
<PDBx:name>NaCl</PDBx:name>
<PDBx:sol_id>2</PDBx:sol_id>
<PDBx:volume>0.200 ml</PDBx:volume>
</PDBx:exptl_crystal_grow_comp>
<PDBx:exptl_crystal_grow_comp crystal_id="1" id="3">
<PDBx:conc>100 mM</PDBx:conc>
<PDBx:details>in 3 mM NaAzide</PDBx:details>
<PDBx:name>Acetic Acid</PDBx:name>
<PDBx:sol_id>2</PDBx:sol_id>
<PDBx:volume>0.047 ml</PDBx:volume>
</PDBx:exptl_crystal_grow_comp>
<PDBx:exptl_crystal_grow_comp crystal_id="1" id="4">
<PDBx:conc>100 mM</PDBx:conc>
<PDBx:details> in 3 mM NaAzide. Buffer components were mixed to produce a
pH of 4.7 according to a ratio calculated from the pKa. The
actual pH of solution 2 was not measured.</PDBx:details>
<PDBx:name>Na Acetate</PDBx:name>
<PDBx:sol_id>2</PDBx:sol_id>
<PDBx:volume>0.053 ml</PDBx:volume>
</PDBx:exptl_crystal_grow_comp>
<PDBx:exptl_crystal_grow_comp crystal_id="1" id="5">
<PDBx:conc>neat</PDBx:conc>
<PDBx:details>in 3 mM NaAzide</PDBx:details>
<PDBx:name>water</PDBx:name>
<PDBx:sol_id>2</PDBx:sol_id>
<PDBx:volume>0.700 ml</PDBx:volume>
</PDBx:exptl_crystal_grow_comp>
</PDBx:exptl_crystal_grow_compCategory>
0
1
0
1
0
1
0
1
0
1
1
1
exptl_crystal_grow_compCategory
This property indicates that datablock
has a category element exptl_crystal_grow_comp.
exptl_crystal_grow_compItem
Abstract Datatype property for exptl_crystal_grow_comp items.
reference_to_exptl_crystal_grow_comp
cross-reference to exptl_crystal_grow_comp
exptl_crystal_grow_comp.conc
The concentration of the solution component.
200 \ml
0.1 ml
exptl_crystal_grow_comp.details
A description of any special aspects of the solution component.
When the solution component is the one that contains the
macromolecule, this could be the specification of the buffer in
which the macromolecule was stored. When the solution component
is a buffer component, this could be the methods (or formula)
used to achieve a desired pH.
in 3 mM NaAzide
The protein solution was in a buffer
containing 25 mM NaCl, 100 mM NaMES/MES
buffer, pH 7.5, 3 mM NaAzide
in 3 mM NaAzide. Buffer components were mixed
to produce a pH of 4.7 according to a ratio
calculated from the pKa. The actual pH of
solution 2 was not measured.
exptl_crystal_grow_comp.name
A common name for the component of the solution.
protein in buffer
acetic acid
exptl_crystal_grow_comp.sol_id
An identifier for the solution to which the given solution
component belongs.
1
well solution
solution A
exptl_crystal_grow_comp.volume
The volume of the solution component.
200 \ml
0.1 ml
exptl_crystal_grow_comp.crystal_id
This data item is a pointer to attribute id in category exptl_crystal in the
EXPTL_CRYSTAL category.
exptl_crystal_grow_comp.id
The value of attribute id in category exptl_crystal_grow_comp must uniquely identify
each item in the EXPTL_CRYSTAL_GROW_COMP list.
Note that this item need not be a number; it can be any unique
identifier.
1
A
protein in buffer
geom
Data items in the GEOM and related (GEOM_ANGLE,
GEOM_BOND, GEOM_CONTACT, GEOM_HBOND and GEOM_TORSION)
categories record details about the molecular
geometry as calculated from the contents of the ATOM, CELL
and SYMMETRY data.
Geometry data are therefore redundant, in that they can be
calculated from other more fundamental quantities in the data
block. However, they provide a check on the correctness of
both sets of data and enable the most important geometric data
to be identified for publication by setting the appropriate
publication flag.
0
1
1
geomCategory
This property indicates that datablock
has a category element geom.
geomItem
Abstract Datatype property for geom items.
reference_to_geom
cross-reference to geom
geom.details
A description of geometry not covered by the
existing data names in the GEOM categories, such as
least-squares planes.
geom.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
geom_angle
Data items in the GEOM_ANGLE category record details about the
bond angles as calculated from the contents
of the ATOM, CELL and SYMMETRY data.
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<PDBx:geom_angleCategory>
<PDBx:geom_angle atom_site_id_1="C2" atom_site_id_2="O1" atom_site_id_3="C5" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555">
<PDBx:publ_flag>yes</PDBx:publ_flag>
<PDBx:value>111.6</PDBx:value>
<PDBx:value_esd>0.2</PDBx:value_esd>
</PDBx:geom_angle>
<PDBx:geom_angle atom_site_id_1="O1" atom_site_id_2="C2" atom_site_id_3="C3" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555">
<PDBx:publ_flag>yes</PDBx:publ_flag>
<PDBx:value>110.9</PDBx:value>
<PDBx:value_esd>0.2</PDBx:value_esd>
</PDBx:geom_angle>
<PDBx:geom_angle atom_site_id_1="O1" atom_site_id_2="C2" atom_site_id_3="O21" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555">
<PDBx:publ_flag>yes</PDBx:publ_flag>
<PDBx:value>122.2</PDBx:value>
<PDBx:value_esd>0.3</PDBx:value_esd>
</PDBx:geom_angle>
<PDBx:geom_angle atom_site_id_1="C3" atom_site_id_2="C2" atom_site_id_3="O21" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555">
<PDBx:publ_flag>yes</PDBx:publ_flag>
<PDBx:value>127.0</PDBx:value>
<PDBx:value_esd>0.3</PDBx:value_esd>
</PDBx:geom_angle>
<PDBx:geom_angle atom_site_id_1="C2" atom_site_id_2="C3" atom_site_id_3="N4" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555">
<PDBx:publ_flag>yes</PDBx:publ_flag>
<PDBx:value>101.3</PDBx:value>
<PDBx:value_esd>0.2</PDBx:value_esd>
</PDBx:geom_angle>
<PDBx:geom_angle atom_site_id_1="C2" atom_site_id_2="C3" atom_site_id_3="C31" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555">
<PDBx:publ_flag>yes</PDBx:publ_flag>
<PDBx:value>111.3</PDBx:value>
<PDBx:value_esd>0.2</PDBx:value_esd>
</PDBx:geom_angle>
<PDBx:geom_angle atom_site_id_1="C2" atom_site_id_2="C3" atom_site_id_3="H3" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555">
<PDBx:publ_flag>no</PDBx:publ_flag>
<PDBx:value>107</PDBx:value>
<PDBx:value_esd>1</PDBx:value_esd>
</PDBx:geom_angle>
<PDBx:geom_angle atom_site_id_1="N4" atom_site_id_2="C3" atom_site_id_3="C31" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555">
<PDBx:publ_flag>yes</PDBx:publ_flag>
<PDBx:value>116.7</PDBx:value>
<PDBx:value_esd>0.2</PDBx:value_esd>
</PDBx:geom_angle>
</PDBx:geom_angleCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
1
1
geom_angleCategory
This property indicates that datablock
has a category element geom_angle.
geom_angleItem
Abstract Datatype property for geom_angle items.
reference_to_geom_angle
cross-reference to geom_angle
geom_angle.atom_site_auth_asym_id_1
An optional identifier of the first of the three atom sites that
define the angle.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_auth_asym_id_2
An optional identifier of the second of the three atom sites
that define the angle.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_auth_asym_id_3
An optional identifier of the third of the three atom sites that
define the angle.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_auth_atom_id_1
An optional identifier of the first of the three atom sites that
define the angle.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_auth_atom_id_2
An optional identifier of the second of the three atom sites
that define the angle.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_auth_atom_id_3
An optional identifier of the third of the three atom sites that
define the angle.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_auth_comp_id_1
An optional identifier of the first of the three atom sites that
define the angle.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_auth_comp_id_2
An optional identifier of the second of the three atom sites
that define the angle.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_auth_comp_id_3
An optional identifier of the third of the three atom sites that
define the angle.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_auth_seq_id_1
An optional identifier of the first of the three atom sites that
define the angle.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_auth_seq_id_2
An optional identifier of the second of the three atom sites
that define the angle.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_auth_seq_id_3
An optional identifier of the third of the three atom sites that
define the angle.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_label_alt_id_1
An optional identifier of the first of the three atom sites that
define the angle.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_label_alt_id_2
An optional identifier of the second of the three atom sites
that define the angle.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_label_alt_id_3
An optional identifier of the third of the three atom sites that
define the angle.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_label_asym_id_1
An optional identifier of the first of the three atom sites that
define the angle.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_label_asym_id_2
An optional identifier of the second of the three atom sites
that define the angle.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_label_asym_id_3
An optional identifier of the third of the three atom sites that
define the angle.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_label_atom_id_1
An optional identifier of the first of the three atom sites that
define the angle.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_label_atom_id_2
An optional identifier of the second of the three atom sites
that define the angle.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_label_atom_id_3
An optional identifier of the third of the three atom sites that
define the angle.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_label_comp_id_1
An optional identifier of the first of the three atom sites that
define the angle.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_label_comp_id_2
An optional identifier of the second of the three atom sites
that define the angle.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_label_comp_id_3
An optional identifier of the third of the three atom sites that
define the angle.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_label_seq_id_1
An optional identifier of the first of the three atom sites that
define the angle.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_label_seq_id_2
An optional identifier of the second of the three atom sites
that define the angle.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
geom_angle.atom_site_label_seq_id_3
An optional identifier of the third of the three atom sites that
define the angle.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
geom_angle.pdbx_PDB_model_num
Pointer to attribute pdbx_PDB_model_num in category atom_site
geom_angle.pdbx_atom_site_PDB_ins_code_1
Pointer to attribute pdbx_PDB_ins_code in category atom_site.
geom_angle.pdbx_atom_site_PDB_ins_code_2
Pointer to attribute pdbx_PDB_ins_code in category atom_site.
geom_angle.pdbx_atom_site_PDB_ins_code_3
Pointer to attribute pdbx_PDB_ins_code in category atom_site.
no
n
yes
y
This code signals whether the angle is referred to in a
publication or should be placed in a table of significant angles.
geom_angle.value
Angle in degrees defined by the three sites
_geom_angle.atom_site_id_1, _geom_angle.atom_site_id_2 and
attribute atom_site_id_3 in category geom_angle.
geom_angle.value_esd
The standard uncertainty (estimated standard deviation)
of attribute value in category geom_angle.
geom_angle.atom_site_id_1
The identifier of the first of the three atom sites that define
the angle.
This data item is a pointer to attribute id in category atom_site in the ATOM_SITE
category.
geom_angle.atom_site_id_2
The identifier of the second of the three atom sites that define
the angle. The second atom is taken to be the apex of the angle.
This data item is a pointer to attribute id in category atom_site in the ATOM_SITE
category.
geom_angle.atom_site_id_3
The identifier of the third of the three atom sites that define
the angle.
This data item is a pointer to attribute id in category atom_site in the ATOM_SITE
category.
geom_angle.site_symmetry_1
The symmetry code of the first of the three atom sites that
define the angle.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
geom_angle.site_symmetry_2
The symmetry code of the second of the three atom sites that
define the angle.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
geom_angle.site_symmetry_3
The symmetry code of the third of the three atom sites that
define the angle.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
geom_bond
Data items in the GEOM_BOND category record details about
the bond lengths as calculated from the contents
of the ATOM, CELL and SYMMETRY data.
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<PDBx:geom_bondCategory>
<PDBx:geom_bond atom_site_id_1="O1" atom_site_id_2="C2" site_symmetry_1="1_555" site_symmetry_2="1_555">
<PDBx:dist>1.342</PDBx:dist>
<PDBx:dist_esd>0.004</PDBx:dist_esd>
<PDBx:publ_flag>yes</PDBx:publ_flag>
</PDBx:geom_bond>
<PDBx:geom_bond atom_site_id_1="O1" atom_site_id_2="C5" site_symmetry_1="1_555" site_symmetry_2="1_555">
<PDBx:dist>1.439</PDBx:dist>
<PDBx:dist_esd>0.003</PDBx:dist_esd>
<PDBx:publ_flag>yes</PDBx:publ_flag>
</PDBx:geom_bond>
<PDBx:geom_bond atom_site_id_1="C2" atom_site_id_2="C3" site_symmetry_1="1_555" site_symmetry_2="1_555">
<PDBx:dist>1.512</PDBx:dist>
<PDBx:dist_esd>0.004</PDBx:dist_esd>
<PDBx:publ_flag>yes</PDBx:publ_flag>
</PDBx:geom_bond>
<PDBx:geom_bond atom_site_id_1="C2" atom_site_id_2="O21" site_symmetry_1="1_555" site_symmetry_2="1_555">
<PDBx:dist>1.199</PDBx:dist>
<PDBx:dist_esd>0.004</PDBx:dist_esd>
<PDBx:publ_flag>yes</PDBx:publ_flag>
</PDBx:geom_bond>
<PDBx:geom_bond atom_site_id_1="C3" atom_site_id_2="N4" site_symmetry_1="1_555" site_symmetry_2="1_555">
<PDBx:dist>1.465</PDBx:dist>
<PDBx:dist_esd>0.003</PDBx:dist_esd>
<PDBx:publ_flag>yes</PDBx:publ_flag>
</PDBx:geom_bond>
<PDBx:geom_bond atom_site_id_1="C3" atom_site_id_2="C31" site_symmetry_1="1_555" site_symmetry_2="1_555">
<PDBx:dist>1.537</PDBx:dist>
<PDBx:dist_esd>0.004</PDBx:dist_esd>
<PDBx:publ_flag>yes</PDBx:publ_flag>
</PDBx:geom_bond>
<PDBx:geom_bond atom_site_id_1="C3" atom_site_id_2="H3" site_symmetry_1="1_555" site_symmetry_2="1_555">
<PDBx:dist>1.00</PDBx:dist>
<PDBx:dist_esd>0.03</PDBx:dist_esd>
<PDBx:publ_flag>no</PDBx:publ_flag>
</PDBx:geom_bond>
<PDBx:geom_bond atom_site_id_1="N4" atom_site_id_2="C5" site_symmetry_1="1_555" site_symmetry_2="1_555">
<PDBx:dist>1.472</PDBx:dist>
<PDBx:dist_esd>0.003</PDBx:dist_esd>
<PDBx:publ_flag>yes</PDBx:publ_flag>
</PDBx:geom_bond>
</PDBx:geom_bondCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
geom_bondCategory
This property indicates that datablock
has a category element geom_bond.
geom_bondItem
Abstract Datatype property for geom_bond items.
reference_to_geom_bond
cross-reference to geom_bond
geom_bond.atom_site_auth_asym_id_1
An optional identifier of the first of the two atom sites that
define the bond.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
geom_bond.atom_site_auth_asym_id_2
An optional identifier of the second of the two atom sites that
define the bond.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
geom_bond.atom_site_auth_atom_id_1
An optional identifier of the first of the two atom sites that
define the bond.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
geom_bond.atom_site_auth_atom_id_2
An optional identifier of the second of the two atom sites that
define the bond.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
geom_bond.atom_site_auth_comp_id_1
An optional identifier of the first of the two atom sites that
define the bond.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
geom_bond.atom_site_auth_comp_id_2
An optional identifier of the second of the two atom sites that
define the bond.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
geom_bond.atom_site_auth_seq_id_1
An optional identifier of the first of the two atom sites that
define the bond.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
geom_bond.atom_site_auth_seq_id_2
An optional identifier of the second of the two atom sites that
define the bond.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
geom_bond.atom_site_label_alt_id_1
An optional identifier of the first of the two atom sites that
define the bond.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
geom_bond.atom_site_label_alt_id_2
An optional identifier of the second of the two atom sites that
define the bond.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
geom_bond.atom_site_label_asym_id_1
An optional identifier of the first of the two atom sites that
define the bond.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
geom_bond.atom_site_label_asym_id_2
An optional identifier of the second of the two atom sites that
define the bond.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
geom_bond.atom_site_label_atom_id_1
An optional identifier of the first of the two atom sites that
define the bond.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
geom_bond.atom_site_label_atom_id_2
An optional identifier of the second of the two atom sites that
define the bond.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
geom_bond.atom_site_label_comp_id_1
An optional identifier of the first of the two atom sites that
define the bond.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
geom_bond.atom_site_label_comp_id_2
An optional identifier of the second of the two atom sites that
define the bond.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
geom_bond.atom_site_label_seq_id_1
An optional identifier of the first of the two atom sites that
define the bond.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
geom_bond.atom_site_label_seq_id_2
An optional identifier of the second of the two atom sites that
define the bond.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
geom_bond.dist
The intramolecular bond distance in angstroms.
geom_bond.dist_esd
The standard uncertainty (estimated standard deviation)
of attribute dist in category geom_bond.
geom_bond.pdbx_PDB_model_num
Pointer to attribute pdbx_PDB_model_num in category atom_site
geom_bond.pdbx_atom_site_PDB_ins_code_1
Pointer to attribute pdbx_PDB_ins_code in category atom_site.
geom_bond.pdbx_atom_site_PDB_ins_code_2
Pointer to attribute pdbx_PDB_ins_code in category atom_site.
no
n
yes
y
This code signals whether the bond distance is referred to in a
publication or should be placed in a list of significant bond
distances.
geom_bond.valence
The bond valence calculated from attribute dist in category geom_bond.
geom_bond.atom_site_id_1
The identifier of the first of the two atom sites that define the
bond.
This data item is a pointer to attribute id in category atom_site in the ATOM_SITE
category.
geom_bond.atom_site_id_2
The identifier of the second of the two atom sites that define
the bond.
This data item is a pointer to attribute id in category atom_site in the ATOM_SITE
category.
geom_bond.site_symmetry_1
The symmetry code of the first of the two atom sites that
define the bond.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
geom_bond.site_symmetry_2
The symmetry code of the second of the two atom sites that
define the bond.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
geom_contact
Data items in the GEOM_CONTACT category record details about
interatomic contacts as calculated from the contents
of the ATOM, CELL and SYMMETRY data.
Example 1 - based on data set CLPHO6 of Ferguson, Ruhl, McKervey & Browne
[Acta Cryst. (1992), C48, 2262-2264].
<PDBx:geom_contactCategory>
<PDBx:geom_contact atom_site_id_1="O(1)" atom_site_id_2="O(2)" site_symmetry_1="1_555" site_symmetry_2="1_555">
<PDBx:dist>2.735</PDBx:dist>
<PDBx:dist_esd>0.003</PDBx:dist_esd>
<PDBx:publ_flag>yes</PDBx:publ_flag>
</PDBx:geom_contact>
<PDBx:geom_contact atom_site_id_1="H(O1)" atom_site_id_2="O(2)" site_symmetry_1="1_555" site_symmetry_2="1_555">
<PDBx:dist>1.82</PDBx:dist>
<PDBx:dist_esd></PDBx:dist_esd>
<PDBx:publ_flag>no</PDBx:publ_flag>
</PDBx:geom_contact>
</PDBx:geom_contactCategory>
0
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1
geom_contactCategory
This property indicates that datablock
has a category element geom_contact.
geom_contactItem
Abstract Datatype property for geom_contact items.
reference_to_geom_contact
cross-reference to geom_contact
geom_contact.atom_site_auth_asym_id_1
An optional identifier of the first of the two atom sites that
define the contact.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
geom_contact.atom_site_auth_asym_id_2
An optional identifier of the second of the two atom sites that
define the contact.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
geom_contact.atom_site_auth_atom_id_1
An optional identifier of the first of the two atom sites that
define the contact.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
geom_contact.atom_site_auth_atom_id_2
An optional identifier of the second of the two atom sites that
define the contact.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
geom_contact.atom_site_auth_comp_id_1
An optional identifier of the first of the two atom sites that
define the contact.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
geom_contact.atom_site_auth_comp_id_2
An optional identifier of the second of the two atom sites that
define the contact.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
geom_contact.atom_site_auth_seq_id_1
An optional identifier of the first of the two atom sites that
define the contact.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
geom_contact.atom_site_auth_seq_id_2
An optional identifier of the second of the two atom sites that
define the contact.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
geom_contact.atom_site_label_alt_id_1
An optional identifier of the first of the two atom sites that
define the contact.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
geom_contact.atom_site_label_alt_id_2
An optional identifier of the second of the two atom sites that
define the contact.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
geom_contact.atom_site_label_asym_id_1
An optional identifier of the first of the two atom sites that
define the contact.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
geom_contact.atom_site_label_asym_id_2
An optional identifier of the second of the two atom sites that
define the contact.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
geom_contact.atom_site_label_atom_id_1
An optional identifier of the first of the two atom sites that
define the contact.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
geom_contact.atom_site_label_atom_id_2
An optional identifier of the second of the two atom sites that
define the contact.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
geom_contact.atom_site_label_comp_id_1
An optional identifier of the first of the two atom sites that
define the contact.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
geom_contact.atom_site_label_comp_id_2
An optional identifier of the second of the two atom sites that
define the contact.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
geom_contact.atom_site_label_seq_id_1
An optional identifier of the first of the two atom sites that
define the contact.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
geom_contact.atom_site_label_seq_id_2
An optional identifier of the second of the two atom sites that
define the contact.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
geom_contact.dist
The interatomic contact distance in angstroms.
geom_contact.dist_esd
The standard uncertainty (estimated standard deviation)
of attribute dist in category geom_contact.
geom_contact.pdbx_PDB_model_num
Pointer to attribute pdbx_PDB_model_num in category atom_site
geom_contact.pdbx_atom_site_PDB_ins_code_1
Pointer to attribute pdbx_PDB_ins_code in category atom_site.
geom_contact.pdbx_atom_site_PDB_ins_code_2
Pointer to attribute pdbx_PDB_ins_code in category atom_site.
no
n
yes
y
This code signals whether the contact distance is referred to
in a publication or should be placed in a list of significant
contact distances.
geom_contact.atom_site_id_1
The identifier of the first of the two atom sites that define the
contact.
This data item is a pointer to attribute id in category atom_site in the ATOM_SITE
category.
geom_contact.atom_site_id_2
The identifier of the second of the two atom sites that define
the contact.
This data item is a pointer to attribute id in category atom_site in the ATOM_SITE
category.
geom_contact.site_symmetry_1
The symmetry code of the first of the two atom sites that
define the contact.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
geom_contact.site_symmetry_2
The symmetry code of the second of the two atom sites that
define the contact.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
geom_hbond
Data items in the GEOM_HBOND category record details about
hydrogen bonds as calculated from the contents of the ATOM,
CELL and SYMMETRY data.
Example 1 - based on C~14~H~13~ClN~2~O.H~2~O, reported by Palmer,
Puddle & Lisgarten [Acta Cryst. (1993), C49, 1777-1779].
<PDBx:geom_hbondCategory>
<PDBx:geom_hbond atom_site_id_A="OW" atom_site_id_D="N6" atom_site_id_H="HN6">
<PDBx:angle_DHA>169.6</PDBx:angle_DHA>
<PDBx:dist_DA>2.801</PDBx:dist_DA>
<PDBx:dist_DH>0.888</PDBx:dist_DH>
<PDBx:dist_HA>1.921</PDBx:dist_HA>
<PDBx:publ_flag>yes</PDBx:publ_flag>
</PDBx:geom_hbond>
<PDBx:geom_hbond atom_site_id_A="O7" atom_site_id_D="OW" atom_site_id_H="HO2">
<PDBx:angle_DHA>153.5</PDBx:angle_DHA>
<PDBx:dist_DA>2.793</PDBx:dist_DA>
<PDBx:dist_DH>0.917</PDBx:dist_DH>
<PDBx:dist_HA>1.923</PDBx:dist_HA>
<PDBx:publ_flag>yes</PDBx:publ_flag>
</PDBx:geom_hbond>
<PDBx:geom_hbond atom_site_id_A="N10" atom_site_id_D="OW" atom_site_id_H="HO1">
<PDBx:angle_DHA>179.7</PDBx:angle_DHA>
<PDBx:dist_DA>2.842</PDBx:dist_DA>
<PDBx:dist_DH>0.894</PDBx:dist_DH>
<PDBx:dist_HA>1.886</PDBx:dist_HA>
<PDBx:publ_flag>yes</PDBx:publ_flag>
</PDBx:geom_hbond>
</PDBx:geom_hbondCategory>
0
1
0
1
0
1
0
1
0
1
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1
0
1
0
1
0
1
0
1
0
1
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0
1
0
1
0
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0
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1
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1
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1
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1
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0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
1
1
geom_hbondCategory
This property indicates that datablock
has a category element geom_hbond.
geom_hbondItem
Abstract Datatype property for geom_hbond items.
reference_to_geom_hbond
cross-reference to geom_hbond
geom_hbond.angle_DHA
The angle in degrees defined by the donor-, hydrogen- and
acceptor-atom sites in a hydrogen bond.
geom_hbond.angle_DHA_esd
The standard uncertainty (estimated standard deviation)
of attribute angle_DHA in category geom_hbond.
geom_hbond.atom_site_auth_asym_id_A
An optional identifier of the acceptor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_auth_asym_id_D
An optional identifier of the donor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_auth_asym_id_H
An optional identifier of the hydrogen-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_auth_atom_id_A
An optional identifier of the acceptor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_auth_atom_id_D
An optional identifier of the donor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_auth_atom_id_H
An optional identifier of the hydrogen-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_auth_comp_id_A
An optional identifier of the acceptor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_auth_comp_id_D
An optional identifier of the donor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_auth_comp_id_H
An optional identifier of the hydrogen-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_auth_seq_id_A
An optional identifier of the acceptor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_auth_seq_id_D
An optional identifier of the donor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_auth_seq_id_H
An optional identifier of the hydrogen-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_label_alt_id_A
An optional identifier of the acceptor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_label_alt_id_D
An optional identifier of the donor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_label_alt_id_H
An optional identifier of the hydrogen-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_label_asym_id_A
An optional identifier of the acceptor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_label_asym_id_D
An optional identifier of the donor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_label_asym_id_H
An optional identifier of the hydrogen-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_label_atom_id_A
An optional identifier of the acceptor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_label_atom_id_D
An optional identifier of the donor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_label_atom_id_H
An optional identifier of the hydrogen-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_label_comp_id_A
An optional identifier of the acceptor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_label_comp_id_D
An optional identifier of the donor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_label_comp_id_H
An optional identifier of the hydrogen-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_label_seq_id_A
An optional identifier of the acceptor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_label_seq_id_D
An optional identifier of the donor-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
geom_hbond.atom_site_label_seq_id_H
An optional identifier of the hydrogen-atom site that defines
the hydrogen bond.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
geom_hbond.dist_DA
The distance in angstroms between the donor- and acceptor-atom
sites in a hydrogen bond.
geom_hbond.dist_DA_esd
The standard uncertainty (estimated standard deviation)
in angstroms of attribute dist_DA in category geom_hbond.
geom_hbond.dist_DH
The distance in angstroms between the donor- and hydrogen-atom
sites in a hydrogen bond.
geom_hbond.dist_DH_esd
The standard uncertainty (estimated standard deviation)
in angstroms of attribute dist_DH in category geom_hbond.
geom_hbond.dist_HA
The distance in angstroms between the hydrogen- and acceptor-
atom sites in a hydrogen bond.
geom_hbond.dist_HA_esd
The standard uncertainty (estimated standard deviation)
in angstroms of attribute dist_HA in category geom_hbond.
no
n
yes
y
This code signals whether the hydrogen-bond information is
referred to in a publication or should be placed in a table of
significant hydrogen-bond geometry.
geom_hbond.atom_site_id_A
The identifier of the acceptor-atom site that defines the
hydrogen bond.
This data item is a pointer to attribute id in category atom_site in the ATOM_SITE
category.
geom_hbond.atom_site_id_D
The identifier of the donor-atom site that defines the hydrogen
bond.
This data item is a pointer to attribute id in category atom_site in the ATOM_SITE
category.
geom_hbond.atom_site_id_H
The identifier of the hydrogen-atom site that defines the
hydrogen bond.
This data item is a pointer to attribute id in category atom_site in the ATOM_SITE
category.
geom_hbond.site_symmetry_A
The symmetry code of the acceptor-atom site that defines the
hydrogen bond.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
geom_hbond.site_symmetry_D
The symmetry code of the donor-atom site that defines the
hydrogen bond.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
geom_hbond.site_symmetry_H
The symmetry code of the hydrogen-atom site that defines the
hydrogen bond.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
geom_torsion
Data items in the GEOM_TORSION category record details about
torsion angles as calculated from the
contents of the ATOM, CELL and SYMMETRY data.
The vector direction attribute atom_site_id_2 in category geom_torsion to
attribute atom_site_id_3 in category geom_torsion is the viewing direction, and the
torsion angle is the angle of twist required to superimpose the
projection of the vector between site 2 and site 1 onto the
projection of the vector between site 3 and site 4. Clockwise
torsions are positive, anticlockwise torsions are negative.
Ref: Klyne, W. & Prelog, V. (1960). Experientia, 16, 521-523.
Example 1 - based on data set CLPHO6 of Ferguson, Ruhl, McKervey & Browne
[Acta Cryst. (1992), C48, 2262-2264].
<PDBx:geom_torsionCategory>
<PDBx:geom_torsion atom_site_id_1="C(9)" atom_site_id_2="O(2)" atom_site_id_3="C(7)" atom_site_id_4="C(2)" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555" site_symmetry_4="1_555">
<PDBx:publ_flag>yes</PDBx:publ_flag>
<PDBx:value>71.8</PDBx:value>
</PDBx:geom_torsion>
<PDBx:geom_torsion atom_site_id_1="C(7)" atom_site_id_2="O(2)" atom_site_id_3="C(9)" atom_site_id_4="C(10)" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555" site_symmetry_4="2_666">
<PDBx:publ_flag>yes</PDBx:publ_flag>
<PDBx:value>-168.0</PDBx:value>
</PDBx:geom_torsion>
<PDBx:geom_torsion atom_site_id_1="C(10)" atom_site_id_2="O(3)" atom_site_id_3="C(8)" atom_site_id_4="C(6)" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555" site_symmetry_4="1_555">
<PDBx:publ_flag>yes</PDBx:publ_flag>
<PDBx:value>-167.7</PDBx:value>
</PDBx:geom_torsion>
<PDBx:geom_torsion atom_site_id_1="C(8)" atom_site_id_2="O(3)" atom_site_id_3="C(10)" atom_site_id_4="C(9)" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555" site_symmetry_4="2_666">
<PDBx:publ_flag>yes</PDBx:publ_flag>
<PDBx:value>-69.7</PDBx:value>
</PDBx:geom_torsion>
<PDBx:geom_torsion atom_site_id_1="O(1)" atom_site_id_2="C(1)" atom_site_id_3="C(2)" atom_site_id_4="C(3)" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555" site_symmetry_4="1_555">
<PDBx:publ_flag>no</PDBx:publ_flag>
<PDBx:value>-179.5</PDBx:value>
</PDBx:geom_torsion>
<PDBx:geom_torsion atom_site_id_1="O(1)" atom_site_id_2="C(1)" atom_site_id_3="C(2)" atom_site_id_4="C(7)" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555" site_symmetry_4="1_555">
<PDBx:publ_flag>no</PDBx:publ_flag>
<PDBx:value>-0.6</PDBx:value>
</PDBx:geom_torsion>
</PDBx:geom_torsionCategory>
0
1
0
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0
1
0
1
1
1
1
1
1
1
1
1
geom_torsionCategory
This property indicates that datablock
has a category element geom_torsion.
geom_torsionItem
Abstract Datatype property for geom_torsion items.
reference_to_geom_torsion
cross-reference to geom_torsion
geom_torsion.atom_site_auth_asym_id_1
An optional identifier of the first of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_auth_asym_id_2
An optional identifier of the second of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_auth_asym_id_3
An optional identifier of the third of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_auth_asym_id_4
An optional identifier of the fourth of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_auth_atom_id_1
An optional identifier of the first of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_auth_atom_id_2
An optional identifier of the second of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_auth_atom_id_3
An optional identifier of the third of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_auth_atom_id_4
An optional identifier of the fourth of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_auth_comp_id_1
An optional identifier of the first of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_auth_comp_id_2
An optional identifier of the second of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_auth_comp_id_3
An optional identifier of the third of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_auth_comp_id_4
An optional identifier of the fourth of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_auth_seq_id_1
An optional identifier of the first of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_auth_seq_id_2
An optional identifier of the second of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_auth_seq_id_3
An optional identifier of the third of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_auth_seq_id_4
An optional identifier of the fourth of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_alt_id_1
An optional identifier of the first of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_alt_id_2
An optional identifier of the second of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_alt_id_3
An optional identifier of the third of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_alt_id_4
An optional identifier of the fourth of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_asym_id_1
An optional identifier of the first of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_asym_id_2
An optional identifier of the second of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_asym_id_3
An optional identifier of the third of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_asym_id_4
An optional identifier of the fourth of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_atom_id_1
An optional identifier of the first of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_atom_id_2
An optional identifier of the second of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_atom_id_3
An optional identifier of the third of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_atom_id_4
An optional identifier of the fourth of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_comp_id_1
An optional identifier of the first of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_comp_id_2
An optional identifier of the second of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_comp_id_3
An optional identifier of the third of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_comp_id_4
An optional identifier of the fourth of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_seq_id_1
An optional identifier of the first of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_seq_id_2
An optional identifier of the second of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_seq_id_3
An optional identifier of the third of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
geom_torsion.atom_site_label_seq_id_4
An optional identifier of the fourth of the four atom sites that
define the torsion angle.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
geom_torsion.pdbx_PDB_model_num
Pointer to attribute pdbx_PDB_model_num in category atom_site
geom_torsion.pdbx_atom_site_PDB_ins_code_1
Pointer to attribute pdbx_PDB_ins_code in category atom_site.
geom_torsion.pdbx_atom_site_PDB_ins_code_2
Pointer to attribute pdbx_PDB_ins_code in category atom_site.
geom_torsion.pdbx_atom_site_PDB_ins_code_3
Pointer to attribute pdbx_PDB_ins_code in category atom_site.
geom_torsion.pdbx_atom_site_PDB_ins_code_4
Pointer to attribute pdbx_PDB_ins_code in category atom_site.
no
n
yes
y
This code signals whether the torsion angle is referred to in a
publication or should be placed in a table of significant
torsion angles.
geom_torsion.value
The value of the torsion angle in degrees.
geom_torsion.value_esd
The standard uncertainty (estimated standard deviation)
of attribute value in category geom_torsion.
geom_torsion.atom_site_id_1
The identifier of the first of the four atom sites that define
the torsion angle.
This data item is a pointer to attribute id in category atom_site in the ATOM_SITE
category.
geom_torsion.atom_site_id_2
The identifier of the second of the four atom sites that define
the torsion angle.
This data item is a pointer to attribute id in category atom_site in the ATOM_SITE
category.
geom_torsion.atom_site_id_3
The identifier of the third of the four atom sites that define
the torsion angle.
This data item is a pointer to attribute id in category atom_site in the ATOM_SITE
category.
geom_torsion.atom_site_id_4
The identifier of the fourth of the four atom sites that define
the torsion angle.
This data item is a pointer to attribute id in category atom_site in the ATOM_SITE
category.
geom_torsion.site_symmetry_1
The symmetry code of the first of the four atom sites that
define the torsion angle.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
geom_torsion.site_symmetry_2
The symmetry code of the second of the four atom sites that
define the torsion angle.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
geom_torsion.site_symmetry_3
The symmetry code of the third of the four atom sites that
define the torsion angle.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
geom_torsion.site_symmetry_4
The symmetry code of the fourth of the four atom sites that
define the torsion angle.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
journal
Data items in the JOURNAL category record details about the
book-keeping by the journal staff when processing
a data block submitted for publication.
The creator of a data block will not normally specify these data.
The data names are not defined in the dictionary because they are
for journal use only.
Example 1 - based on Acta Cryst. file for entry HL0007 [Willis, Beckwith
& Tozer (1991). Acta Cryst. C47, 2276-2277].
<PDBx:journalCategory>
<PDBx:journal entry_id="TOZ">
<PDBx:coden_ASTM>ACSCEE</PDBx:coden_ASTM>
<PDBx:coeditor_code>HL0007</PDBx:coeditor_code>
<PDBx:date_accepted>1991-04-18</PDBx:date_accepted>
<PDBx:date_from_coeditor>1991-04-18</PDBx:date_from_coeditor>
<PDBx:date_printers_first>1991-08-07</PDBx:date_printers_first>
<PDBx:date_proofs_out>1991-08-07</PDBx:date_proofs_out>
<PDBx:date_recd_electronic>1991-04-15</PDBx:date_recd_electronic>
<PDBx:issue>NOV91</PDBx:issue>
<PDBx:name_full>Acta Crystallographica Section C</PDBx:name_full>
<PDBx:page_first>2276</PDBx:page_first>
<PDBx:page_last>2277</PDBx:page_last>
<PDBx:techeditor_code>C910963</PDBx:techeditor_code>
<PDBx:volume>47</PDBx:volume>
<PDBx:year>1991</PDBx:year>
</PDBx:journal>
</PDBx:journalCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
journalCategory
This property indicates that datablock
has a category element journal.
journalItem
Abstract Datatype property for journal items.
reference_to_journal
cross-reference to journal
journal.coden_ASTM
Journal data items are defined by the journal staff.
journal.coden_Cambridge
Journal data items are defined by the journal staff.
journal.coeditor_address
Journal data items are defined by the journal staff.
journal.coeditor_code
Journal data items are defined by the journal staff.
journal.coeditor_email
Journal data items are defined by the journal staff.
journal.coeditor_fax
Journal data items are defined by the journal staff.
journal.coeditor_name
Journal data items are defined by the journal staff.
journal.coeditor_notes
Journal data items are defined by the journal staff.
journal.coeditor_phone
Journal data items are defined by the journal staff.
journal.data_validation_number
Journal data items are defined by the journal staff.
journal.date_accepted
Journal data items are defined by the journal staff.
journal.date_from_coeditor
Journal data items are defined by the journal staff.
journal.date_printers_final
Journal data items are defined by the journal staff.
journal.date_printers_first
Journal data items are defined by the journal staff.
journal.date_proofs_in
Journal data items are defined by the journal staff.
journal.date_proofs_out
Journal data items are defined by the journal staff.
journal.date_recd_copyright
Journal data items are defined by the journal staff.
journal.date_recd_electronic
Journal data items are defined by the journal staff.
journal.date_recd_hard_copy
Journal data items are defined by the journal staff.
journal.date_to_coeditor
Journal data items are defined by the journal staff.
journal.issue
Journal data items are defined by the journal staff.
journal.language
Journal data items are defined by the journal staff.
journal.name_full
Journal data items are defined by the journal staff.
journal.page_first
Journal data items are defined by the journal staff.
journal.page_last
Journal data items are defined by the journal staff.
journal.paper_category
Journal data items are defined by the journal staff.
journal.suppl_publ_number
Journal data items are defined by the journal staff.
journal.suppl_publ_pages
Journal data items are defined by the journal staff.
journal.techeditor_address
Journal data items are defined by the journal staff.
journal.techeditor_code
Journal data items are defined by the journal staff.
journal.techeditor_email
Journal data items are defined by the journal staff.
journal.techeditor_fax
Journal data items are defined by the journal staff.
journal.techeditor_name
Journal data items are defined by the journal staff.
journal.techeditor_notes
Journal data items are defined by the journal staff.
journal.techeditor_phone
Journal data items are defined by the journal staff.
journal.volume
Journal data items are defined by the journal staff.
journal.year
Journal data items are defined by the journal staff.
journal.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
journal_index
Data items in the JOURNAL_INDEX category are used to list terms
used to generate the journal indexes.
The creator of a data block will not normally specify these data
items.
Example 1 - based on a paper by Zhu, Reynolds, Klein & Trudell
[Acta Cryst. (1994), C50, 2067-2069].
<PDBx:journal_indexCategory>
<PDBx:journal_index term="C16H19NO4" type="O">
<PDBx:subterm></PDBx:subterm>
</PDBx:journal_index>
<PDBx:journal_index term="alkaloids" type="S">
<PDBx:subterm>(-)-norcocaine</PDBx:subterm>
</PDBx:journal_index>
<PDBx:journal_index term="(-)-norcocaine" type="S">
<PDBx:subterm></PDBx:subterm>
</PDBx:journal_index>
<PDBx:journal_index term=" [2R,3S-(2\b,3\b)]-methyl 3-(benzoyloxy)-8-azabicyclo[3.2.1]octane-2-carboxylate" type="S">
<PDBx:subterm></PDBx:subterm>
</PDBx:journal_index>
</PDBx:journal_indexCategory>
0
1
1
1
journal_indexCategory
This property indicates that datablock
has a category element journal_index.
journal_indexItem
Abstract Datatype property for journal_index items.
reference_to_journal_index
cross-reference to journal_index
journal_index.subterm
Journal index data items are defined by the journal staff.
journal_index.term
Journal index data items are defined by the journal staff.
journal_index.type
Journal index data items are defined by the journal staff.
ndb_original_ndb_coordinates
Placeholder category for PDB coordinate data.
1
ndb_original_ndb_coordinatesCategory
This property indicates that datablock
has a category element ndb_original_ndb_coordinates.
ndb_original_ndb_coordinatesItem
Abstract Datatype property for ndb_original_ndb_coordinates items.
reference_to_ndb_original_ndb_coordinates
cross-reference to ndb_original_ndb_coordinates
ndb_original_ndb_coordinates.coord_section
Placeholder item to hold unparsed coordinate data.
ndb_struct_conf_na
Data items in the NDB_STRUCT_CONF_NA category
describes secondary structure features in this entry.
0
1
1
1
ndb_struct_conf_naCategory
This property indicates that datablock
has a category element ndb_struct_conf_na.
ndb_struct_conf_naItem
Abstract Datatype property for ndb_struct_conf_na items.
reference_to_ndb_struct_conf_na
cross-reference to ndb_struct_conf_na
ndb_struct_conf_na.feature_count
This data item counts the number of occurences of
this feature in this entry.
ndb_struct_conf_na.entry_id
This data item is a pointer to attribute id in category entry in the
ENTRY category.
double helix
a-form double helix
b-form double helix
z-form double helix
other right-handed double helix
triple helix
quadruple helix
parallel strands
internal loop
bulge loop
tetraloop
hairpin loop
two-way junction
three-way junction
four-way junction
mismatched base pair
This data item identifies a secondary structure
feature of this entry.
ndb_struct_feature_na
Data items in the NDB_STRUCT_FEATURE_NA category
describes tertiary and other special structural
features in this entry.
0
1
1
1
ndb_struct_feature_naCategory
This property indicates that datablock
has a category element ndb_struct_feature_na.
ndb_struct_feature_naItem
Abstract Datatype property for ndb_struct_feature_na items.
reference_to_ndb_struct_feature_na
cross-reference to ndb_struct_feature_na
ndb_struct_feature_na.feature_count
This data item counts the number of occurences of
this feature in this entry.
ndb_struct_feature_na.entry_id
This data item is a pointer to attribute id in category entry in the
ENTRY category.
pseudoknot
intercalated base
backbone turn
intramolecular base triplet
ribose zipper
purine platform
bent/kinked double helix
This data item identifies a structural
feature of this entry.
ndb_struct_na_base_pair
Data items in the NDB_STRUCT_NA_BASE_PAIR category record details
of base pairing interactions.
<PDBx:ndb_struct_na_base_pairCategory>
<PDBx:ndb_struct_na_base_pair i_label_asym_id="A" i_label_comp_id="G" i_label_seq_id="1" i_symmetry="1_555" j_label_asym_id="A" j_label_comp_id="C" j_label_seq_id="8" j_symmetry="7_555" model_number="1">
<PDBx:buckle>-5.523</PDBx:buckle>
<PDBx:opening>-3.291</PDBx:opening>
<PDBx:propeller>-6.752</PDBx:propeller>
<PDBx:shear>-0.396</PDBx:shear>
<PDBx:stagger>-0.018</PDBx:stagger>
<PDBx:stretch>-0.156</PDBx:stretch>
</PDBx:ndb_struct_na_base_pair>
<PDBx:ndb_struct_na_base_pair i_label_asym_id="A" i_label_comp_id="G" i_label_seq_id="2" i_symmetry="1_555" j_label_asym_id="A" j_label_comp_id="C" j_label_seq_id="7" j_symmetry="7_555" model_number="1">
<PDBx:buckle>-4.727</PDBx:buckle>
<PDBx:opening>2.311</PDBx:opening>
<PDBx:propeller>-9.765</PDBx:propeller>
<PDBx:shear>-0.094</PDBx:shear>
<PDBx:stagger>-0.334</PDBx:stagger>
<PDBx:stretch>-0.220</PDBx:stretch>
</PDBx:ndb_struct_na_base_pair>
<PDBx:ndb_struct_na_base_pair i_label_asym_id="A" i_label_comp_id="G" i_label_seq_id="3" i_symmetry="1_555" j_label_asym_id="A" j_label_comp_id="C" j_label_seq_id="6" j_symmetry="7_555" model_number="1">
<PDBx:buckle>-6.454</PDBx:buckle>
<PDBx:opening>-1.181</PDBx:opening>
<PDBx:propeller>-12.575</PDBx:propeller>
<PDBx:shear>-0.285</PDBx:shear>
<PDBx:stagger>0.008</PDBx:stagger>
<PDBx:stretch>-0.239</PDBx:stretch>
</PDBx:ndb_struct_na_base_pair>
</PDBx:ndb_struct_na_base_pairCategory>
0
1
0
1
0
1
0
1
1
1
1
1
0
1
1
1
1
1
0
1
1
1
1
1
0
1
0
1
0
1
0
1
1
1
1
1
1
1
1
1
1
ndb_struct_na_base_pairCategory
This property indicates that datablock
has a category element ndb_struct_na_base_pair.
ndb_struct_na_base_pairItem
Abstract Datatype property for ndb_struct_na_base_pair items.
reference_to_ndb_struct_na_base_pair
cross-reference to ndb_struct_na_base_pair
ndb_struct_na_base_pair.buckle
The value of the base pair buckle parameter.
ndb_struct_na_base_pair.hbond_type_12
Base pair classification of Westhoff and Leontis.
ndb_struct_na_base_pair.hbond_type_28
Base pair classification of Saenger
ndb_struct_na_base_pair.i_PDB_ins_code
Describes the PDB insertion code of the i-th base in the base pair.
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair.i_auth_asym_id
Describes the asym id of the i-th base in the base pair.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair.i_auth_seq_id
Describes the sequence number of the i-th base in the base pair.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair.j_PDB_ins_code
Describes the PDB insertion code of the j-th base in the base pair.
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair.j_auth_asym_id
Describes the asym id of the j-th base in the base pair.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair.j_auth_seq_id
Describes the sequence number of the j-th base in the base pair.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair.opening
The value of the base pair opening parameter.
ndb_struct_na_base_pair.pair_name
Text label for this base pair.
ndb_struct_na_base_pair.pair_number
Sequential number of pair in the pair sequence.
ndb_struct_na_base_pair.propeller
The value of the base pair propeller parameter.
ndb_struct_na_base_pair.shear
The value of the base pair shear parameter.
ndb_struct_na_base_pair.stagger
The value of the base pair stagger parameter.
ndb_struct_na_base_pair.stretch
The value of the base pair stretch parameter.
ndb_struct_na_base_pair.i_label_asym_id
Describes the asym id of the i-th base in the base pair.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair.i_label_comp_id
Describes the component id of the i-th base in the base pair.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair.i_label_seq_id
Describes the sequence number of the i-th base in the base pair.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair.i_symmetry
Describes the symmetry operation that should be applied to the
coordinates of the i-th base to generate the first partner
in the base pair.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
ndb_struct_na_base_pair.j_label_asym_id
Describes the asym id of the j-th base in the base pair.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair.j_label_comp_id
Describes the component id of the j-th base in the base pair.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair.j_label_seq_id
Describes the sequence number of the j-th base in the base pair.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair.j_symmetry
Describes the symmetry operation that should be applied to the
coordinates of the j-th base to generate the second partner
in the base pair.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
ndb_struct_na_base_pair.model_number
Describes the model number of the the base pair.
This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step
Data items in the NDB_STRUCT_NA_BASE_PAIR_STEP category record details
of base pair step interactions.
<PDBx:ndb_struct_na_base_pair_stepCategory>
<PDBx:ndb_struct_na_base_pair_step i_label_asym_id_1="A" i_label_asym_id_2="A" i_label_comp_id_1="G" i_label_comp_id_2="G" i_label_seq_id_1="1" i_label_seq_id_2="2" i_symmetry_1="1_555" i_symmetry_2="1_555" j_label_asym_id_1="A" j_label_asym_id_2="A" j_label_comp_id_1="C" j_label_comp_id_2="C" j_label_seq_id_1="8" j_label_seq_id_2="7" j_symmetry_1="7_555" j_symmetry_2="7_555" model_number="1">
<PDBx:rise>3.339</PDBx:rise>
<PDBx:roll>9.755</PDBx:roll>
<PDBx:shift>0.369</PDBx:shift>
<PDBx:slide>-1.414</PDBx:slide>
<PDBx:tilt>3.056</PDBx:tilt>
<PDBx:twist>33.530</PDBx:twist>
</PDBx:ndb_struct_na_base_pair_step>
<PDBx:ndb_struct_na_base_pair_step i_label_asym_id_1="A" i_label_asym_id_2="A" i_label_comp_id_1="G" i_label_comp_id_2="G" i_label_seq_id_1="2" i_label_seq_id_2="3" i_symmetry_1="1_555" i_symmetry_2="1_555" j_label_asym_id_1="A" j_label_asym_id_2="A" j_label_comp_id_1="C" j_label_comp_id_2="C" j_label_seq_id_1="7" j_label_seq_id_2="6" j_symmetry_1="7_555" j_symmetry_2="7_555" model_number="1">
<PDBx:rise>3.371</PDBx:rise>
<PDBx:roll>6.725</PDBx:roll>
<PDBx:shift>0.176</PDBx:shift>
<PDBx:slide>-1.672</PDBx:slide>
<PDBx:tilt>-1.176</PDBx:tilt>
<PDBx:twist>30.004</PDBx:twist>
</PDBx:ndb_struct_na_base_pair_step>
</PDBx:ndb_struct_na_base_pair_stepCategory>
0
1
0
1
0
1
0
1
1
1
1
1
1
1
1
1
0
1
0
1
0
1
1
1
1
1
1
1
1
1
0
1
0
1
0
1
0
1
1
1
1
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
ndb_struct_na_base_pair_stepCategory
This property indicates that datablock
has a category element ndb_struct_na_base_pair_step.
ndb_struct_na_base_pair_stepItem
Abstract Datatype property for ndb_struct_na_base_pair_step items.
reference_to_ndb_struct_na_base_pair_step
cross-reference to ndb_struct_na_base_pair_step
ndb_struct_na_base_pair_step.helical_rise
The value of the base pair step helical rise parameter.
ndb_struct_na_base_pair_step.helical_twist
The value of the base pair step helical twist parameter.
ndb_struct_na_base_pair_step.i_PDB_ins_code_1
Describes the PDB insertion code of the i-th base in the
first base pair of the step.
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in
the ATOM_SITE category.
ndb_struct_na_base_pair_step.i_PDB_ins_code_2
Describes the PDB insertion code of the i-th base in the
second base pair of the step.
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in
the ATOM_SITE category.
ndb_struct_na_base_pair_step.i_auth_asym_id_1
Describes the author's asym id of the i-th base in the first
base pair of the step.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.i_auth_asym_id_2
Describes the author's asym id of the i-th base in the second
base pair of the step.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.i_auth_seq_id_1
Describes the author's sequence number of the i-th base in the
first base pair of the step.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.i_auth_seq_id_2
Describes the author's sequence number of the i-th base in the
second base pair of the step.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.inclination
The value of the base pair step inclination parameter.
ndb_struct_na_base_pair_step.j_PDB_ins_code_1
Describes the PDB insertion code of the j-th base in the
first base pair of the step.
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in
the ATOM_SITE category.
ndb_struct_na_base_pair_step.j_PDB_ins_code_2
Describes the PDB insertion code of the j-th base in the
second base pair of the step.
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in
the ATOM_SITE category.
ndb_struct_na_base_pair_step.j_auth_asym_id_1
Describes the author's asym id of the j-th base in the first
base pair of the step.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.j_auth_asym_id_2
Describes the author's asym id of the j-th base in the second
base pair of the step.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.j_auth_seq_id_1
Describes the author's sequence number of the j-th base in the
first base pair of the step.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.j_auth_seq_id_2
Describes the author's sequence number of the j-th base in the
second base pair of the step.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.rise
The value of the base pair step rise parameter.
ndb_struct_na_base_pair_step.roll
The value of the base pair step roll parameter.
ndb_struct_na_base_pair_step.shift
The value of the base pair step shift parameter.
ndb_struct_na_base_pair_step.slide
The value of the base pair step slide parameter.
ndb_struct_na_base_pair_step.step_name
The text name of this step.
ndb_struct_na_base_pair_step.step_number
The sequence number of this step in the step sequence.
ndb_struct_na_base_pair_step.tilt
The value of the base pair step tilt parameter.
ndb_struct_na_base_pair_step.tip
The value of the base pair step twist parameter.
ndb_struct_na_base_pair_step.twist
The value of the base pair step twist parameter.
ndb_struct_na_base_pair_step.x_displacement
The value of the base pair step X displacement parameter.
ndb_struct_na_base_pair_step.y_displacement
The value of the base pair step Y displacement parameter.
ndb_struct_na_base_pair_step.i_label_asym_id_1
Describes the asym id of the i-th base in the first base pair
of the step.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.i_label_asym_id_2
Describes the asym id of the i-th base in the second base pair
of the step.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.i_label_comp_id_1
Describes the component id of the i-th base in the first base pair
of the step.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.i_label_comp_id_2
Describes the component id of the i-th base in the second base pair
of the step.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.i_label_seq_id_1
Describes the sequence number of the i-th base in the first base pair
of the step.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.i_label_seq_id_2
Describes the sequence number of the i-th base in the second base pair
of the step.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.i_symmetry_1
Describes the symmetry operation that should be applied to the
coordinates of the i-th base to generate the first partner
in the first base pair of the step.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
ndb_struct_na_base_pair_step.i_symmetry_2
Describes the symmetry operation that should be applied to the
coordinates of the i-th base to generate the first partner
in the second base pair of the step.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
ndb_struct_na_base_pair_step.j_label_asym_id_1
Describes the asym id of the j-th base in the first base pair
of the step.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.j_label_asym_id_2
Describes the asym id of the j-th base in the second base pair
of the step.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.j_label_comp_id_1
Describes the component id of the j-th base in the first base pair
of the step.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.j_label_comp_id_2
Describes the component id of the j-th base in the second base pair
of the step.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.j_label_seq_id_1
Describes the sequence number of the j-th base in the first base pair
of the step.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.j_label_seq_id_2
Describes the sequence number of the j-th base in the second base pair
of the step.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
ndb_struct_na_base_pair_step.j_symmetry_1
Describes the symmetry operation that should be applied to the
coordinates of the j-th base to generate the second partner
in the first base pair of the step.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
ndb_struct_na_base_pair_step.j_symmetry_2
Describes the symmetry operation that should be applied to the
coordinates of the j-th base to generate the second partner
in the second base pair of the step.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
ndb_struct_na_base_pair_step.model_number
Describes the model number of the the base pair step.
This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the
ATOM_SITE category.
pdbx_SG_project
Data items in the PDBX_CONTACT_AUTHOR category record details
about the Structural Genomics Project and name and initials
for each Center.
Example 1 -
<PDBx:pdbx_SG_projectCategory>
<PDBx:pdbx_SG_project id="1">
<PDBx:full_name_of_center>Berkeley Structural Genomics Center</PDBx:full_name_of_center>
<PDBx:initial_of_center>BSGC</PDBx:initial_of_center>
<PDBx:project_name>PSI, Protein Structure Initiative</PDBx:project_name>
</PDBx:pdbx_SG_project>
</PDBx:pdbx_SG_projectCategory>
0
1
0
1
0
1
1
pdbx_SG_projectCategory
This property indicates that datablock
has a category element pdbx_SG_project.
pdbx_SG_projectItem
Abstract Datatype property for pdbx_SG_project items.
reference_to_pdbx_SG_project
cross-reference to pdbx_SG_project
Accelerated Technologies Center for Gene to 3D Structure
Bacterial targets at IGS-CNRS, France
Berkeley Structural Genomics Center
Center for Eukaryotic Structural Genomics
Center for High-Throughput Structural Biology
Center for Structural Genomics of Infectious Diseases
Center for Structures of Membrane Proteins
Integrated Center for Structure and Function Innovation
Israel Structural Proteomics Center
Joint Center for Structural Genomics
Marseilles Structural Genomics Program @ AFMB
Medical Structural Genomics of Pathogenic Protozoa
Midwest Center for Structural Genomics
Montreal-Kingston Bacterial Structural Genomics Initiative
Mycobacterium Tuberculosis Structural Proteomics Project
New York Consortium on Membrane Protein Structure
New York Structural Genomics Research Consortium
New York Structural GenomiX Research Consortium
New York SGX Research Center for Structural Genomics
Northeast Structural Genomics Consortium
Ontario Centre for Structural Proteomics
Oxford Protein Production Facility
Paris-Sud Yeast Structural Genomics
Protein Structure Factory
RIKEN Structural Genomics/Proteomics Initiative
Scottish Structural Proteomics Facility
Seattle Structural Genomics Center for Infectious Disease
Southeast Collaboratory for Structural Genomics
Structural Genomics Consortium
Structural Genomics Consortium for Research on Gene Expression
Structural Genomics of Pathogenic Protozoa Consortium
Structural Proteomics in Europe
Structural Proteomics in Europe 2
Structure 2 Function Project
The Integrated Center for Structure and Function Innovation
TB Structural Genomics Consortium
The value identifies the full name of center.
Berkeley Structural Genomics Center
ATCG3D
BIGS
BSGC
CESG
CHTSB
CSMP
CSGID
ISFI
ISPC
JCSG
MSGP
MCSG
MSGPP
BSGI
XMTB
NYCOMPS
NYSGRC
NYSGXRC
NESG
OPPF
YSG
PSF
OCSP
RSGI
SECSG
SGC
SGPP
SSGCID
SGCGES
SPINE
SPINE-2
SSPF
S2F
TBSGC
The value identifies the full name of center.
BSGC
PSI, Protein Structure Initiative
NPPSFA, National Project on Protein Structural and Functional Analyses
The value identifies the Structural Genomics project.
PSI, Protein Structure Initiative
1
2
3
4
5
6
7
8
9
10
A unique integer identifier for this center
1 2 3
pdbx_atom_site_aniso_tls
Data items in the PDBX_ATOM_SITE_ANISO_TLS category record details
about the TLS contribution to anisotropic displacement parameters.
Example 1
<PDBx:pdbx_atom_site_aniso_tlsCategory>
<PDBx:pdbx_atom_site_aniso_tls id="1" tls_group_id="1">
<PDBx:U_tls11>2541</PDBx:U_tls11>
<PDBx:U_tls12>676</PDBx:U_tls12>
<PDBx:U_tls13>-827</PDBx:U_tls13>
<PDBx:U_tls22>2835</PDBx:U_tls22>
<PDBx:U_tls23>341</PDBx:U_tls23>
<PDBx:U_tls33>3175</PDBx:U_tls33>
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_atom_id>CB</PDBx:auth_atom_id>
<PDBx:auth_comp_id>SER</PDBx:auth_comp_id>
<PDBx:auth_seq_id>8</PDBx:auth_seq_id>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:pdbx_atom_site_aniso_tls>
<PDBx:pdbx_atom_site_aniso_tls id="2" tls_group_id="1">
<PDBx:U_tls11>3708</PDBx:U_tls11>
<PDBx:U_tls12>633</PDBx:U_tls12>
<PDBx:U_tls13>-724</PDBx:U_tls13>
<PDBx:U_tls22>3876</PDBx:U_tls22>
<PDBx:U_tls23>342</PDBx:U_tls23>
<PDBx:U_tls33>4181</PDBx:U_tls33>
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_atom_id>OG</PDBx:auth_atom_id>
<PDBx:auth_comp_id>SER</PDBx:auth_comp_id>
<PDBx:auth_seq_id>8</PDBx:auth_seq_id>
<PDBx:type_symbol>O</PDBx:type_symbol>
</PDBx:pdbx_atom_site_aniso_tls>
<PDBx:pdbx_atom_site_aniso_tls id="3" tls_group_id="1">
<PDBx:U_tls11>7054</PDBx:U_tls11>
<PDBx:U_tls12>619</PDBx:U_tls12>
<PDBx:U_tls13>-966</PDBx:U_tls13>
<PDBx:U_tls22>7457</PDBx:U_tls22>
<PDBx:U_tls23>344</PDBx:U_tls23>
<PDBx:U_tls33>7553</PDBx:U_tls33>
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_atom_id>C</PDBx:auth_atom_id>
<PDBx:auth_comp_id>SER</PDBx:auth_comp_id>
<PDBx:auth_seq_id>8</PDBx:auth_seq_id>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:pdbx_atom_site_aniso_tls>
<PDBx:pdbx_atom_site_aniso_tls id="4" tls_group_id="1">
<PDBx:U_tls11>6837</PDBx:U_tls11>
<PDBx:U_tls12>567</PDBx:U_tls12>
<PDBx:U_tls13>-974</PDBx:U_tls13>
<PDBx:U_tls22>7210</PDBx:U_tls22>
<PDBx:U_tls23>341</PDBx:U_tls23>
<PDBx:U_tls33>7184</PDBx:U_tls33>
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_atom_id>O</PDBx:auth_atom_id>
<PDBx:auth_comp_id>SER</PDBx:auth_comp_id>
<PDBx:auth_seq_id>8</PDBx:auth_seq_id>
<PDBx:type_symbol>O</PDBx:type_symbol>
</PDBx:pdbx_atom_site_aniso_tls>
<PDBx:pdbx_atom_site_aniso_tls id="5" tls_group_id="1">
<PDBx:U_tls11>5792</PDBx:U_tls11>
<PDBx:U_tls12>538</PDBx:U_tls12>
<PDBx:U_tls13>-778</PDBx:U_tls13>
<PDBx:U_tls22>6180</PDBx:U_tls22>
<PDBx:U_tls23>290</PDBx:U_tls23>
<PDBx:U_tls33>6271</PDBx:U_tls33>
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_atom_id>N</PDBx:auth_atom_id>
<PDBx:auth_comp_id>SER</PDBx:auth_comp_id>
<PDBx:auth_seq_id>8</PDBx:auth_seq_id>
<PDBx:type_symbol>N</PDBx:type_symbol>
</PDBx:pdbx_atom_site_aniso_tls>
<PDBx:pdbx_atom_site_aniso_tls id="6" tls_group_id="1">
<PDBx:U_tls11>8440</PDBx:U_tls11>
<PDBx:U_tls12>616</PDBx:U_tls12>
<PDBx:U_tls13>-861</PDBx:U_tls13>
<PDBx:U_tls22>8771</PDBx:U_tls22>
<PDBx:U_tls23>331</PDBx:U_tls23>
<PDBx:U_tls33>8935</PDBx:U_tls33>
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_atom_id>CA</PDBx:auth_atom_id>
<PDBx:auth_comp_id>SER</PDBx:auth_comp_id>
<PDBx:auth_seq_id>8</PDBx:auth_seq_id>
<PDBx:type_symbol>C</PDBx:type_symbol>
</PDBx:pdbx_atom_site_aniso_tls>
</PDBx:pdbx_atom_site_aniso_tlsCategory>
0
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
0
1
0
1
0
1
0
1
1
1
1
1
pdbx_atom_site_aniso_tlsCategory
This property indicates that datablock
has a category element pdbx_atom_site_aniso_tls.
pdbx_atom_site_aniso_tlsItem
Abstract Datatype property for pdbx_atom_site_aniso_tls items.
reference_to_pdbx_atom_site_aniso_tls
cross-reference to pdbx_atom_site_aniso_tls
pdbx_atom_site_aniso_tls.PDB_ins_code
This data item is a pointer to attribute pdbx_ins_code in category atom_site in the
ATOM_SITE category.
pdbx_atom_site_aniso_tls.U_tls11
The [1][1] element of the TLS contribution to the atomic
displacement matrix U.
The unique elements of the real symmetric matrix are
entered by row.
pdbx_atom_site_aniso_tls.U_tls12
The [1][2] element of the TLS contribution to the atomic
displacement matrix U.
The unique elements of the real symmetric matrix are
entered by row.
pdbx_atom_site_aniso_tls.U_tls13
The [1][3] element of the TLS contribution to the atomic
displacement matrix U.
The unique elements of the real symmetric matrix are
entered by row.
pdbx_atom_site_aniso_tls.U_tls22
The [2][2] element of the TLS contribution to the atomic
displacement matrix U.
The unique elements of the real symmetric matrix are
entered by row.
pdbx_atom_site_aniso_tls.U_tls23
The [2][3] element of the TLS contribution to the atomic
displacement matrix U.
The unique elements of the real symmetric matrix are
entered by row.
pdbx_atom_site_aniso_tls.U_tls33
The [3][3] element of the TLS contribution to the atomic
displacement matrix U.
The unique elements of the real symmetric matrix are
entered by row.
pdbx_atom_site_aniso_tls.auth_asym_id
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_atom_site_aniso_tls.auth_atom_id
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
pdbx_atom_site_aniso_tls.auth_comp_id
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_atom_site_aniso_tls.auth_seq_id
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_atom_site_aniso_tls.label_alt_id
This data item is a pointer to attribute id in category atom_sites_alt in the
ATOM_SITE category.
pdbx_atom_site_aniso_tls.label_asym_id
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_atom_site_aniso_tls.label_atom_id
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
pdbx_atom_site_aniso_tls.label_comp_id
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_atom_site_aniso_tls.label_seq_id
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_atom_site_aniso_tls.type_symbol
This data item is a pointer to attribute symbol in category atom_type in the
ATOM_TYPE category.
pdbx_atom_site_aniso_tls.id
This data item is a pointer to attribute id in category atom_site in the ATOM_SITE
category.
pdbx_atom_site_aniso_tls.tls_group_id
This data item identifies the TLS group membership for
this atom.
pdbx_audit
The PDBX_AUDIT holds current version information.
1
1
1
pdbx_auditCategory
This property indicates that datablock
has a category element pdbx_audit.
pdbx_auditItem
Abstract Datatype property for pdbx_audit items.
reference_to_pdbx_audit
cross-reference to pdbx_audit
pdbx_audit.current_version
The value of attribute entry_id in category pdbx_audit identifies the data block.
1
pdbx_audit.entry_id
The value of attribute entry_id in category pdbx_audit identifies the data block.
BDL001
pdbx_audit_author
Data items in the PDBX_AUDIT_AUTHOR category record details about
the author(s) of the data block.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
<PDBx:pdbx_audit_authorCategory>
<PDBx:pdbx_audit_author ordinal="1">
<PDBx:address> Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA</PDBx:address>
<PDBx:name>Fitzgerald, Paula M.D.</PDBx:name>
</PDBx:pdbx_audit_author>
<PDBx:pdbx_audit_author ordinal="2">
<PDBx:address> Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA</PDBx:address>
<PDBx:name>McKeever, Brian M.</PDBx:name>
</PDBx:pdbx_audit_author>
<PDBx:pdbx_audit_author ordinal="3">
<PDBx:address> Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA</PDBx:address>
<PDBx:name>Van Middlesworth, J.F.</PDBx:name>
</PDBx:pdbx_audit_author>
<PDBx:pdbx_audit_author ordinal="4">
<PDBx:address> Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA</PDBx:address>
<PDBx:name>Springer, James P.</PDBx:name>
</PDBx:pdbx_audit_author>
</PDBx:pdbx_audit_authorCategory>
0
1
1
1
1
pdbx_audit_authorCategory
This property indicates that datablock
has a category element pdbx_audit_author.
pdbx_audit_authorItem
Abstract Datatype property for pdbx_audit_author items.
reference_to_pdbx_audit_author
cross-reference to pdbx_audit_author
pdbx_audit_author.address
The address of an author of this data block. If there are
multiple authors, attribute address in category pdbx_audit_author is looped with
attribute name in category pdbx_audit_author.
Department
Institute
Street
City and postcode
COUNTRY
pdbx_audit_author.name
The name of an author of this data block. If there are multiple
authors, _pdbx_audit_author.name is looped with _pdbx_audit_author.address.
The family name(s), followed by a comma and including any
dynastic compoents, precedes the first name(s) or initial(s).
Bleary, Percival R.
O'Neil, F.K.
Van den Bossche, G.
Yang, D.-L.
Simonov, Yu.A
pdbx_audit_author.ordinal
A unique sequential integer identifier for each author.
1
2
3
pdbx_buffer
Data items in the PDBX_BUFFER category
record details of the sample buffer.
0
1
0
1
1
pdbx_bufferCategory
This property indicates that datablock
has a category element pdbx_buffer.
pdbx_bufferItem
Abstract Datatype property for pdbx_buffer items.
reference_to_pdbx_buffer
cross-reference to pdbx_buffer
pdbx_buffer.details
Any additional details to do with buffer.
aerated
pdbx_buffer.name
The name of each buffer.
Acetic acid
pdbx_buffer.id
The value of attribute id in category pdbx_buffer must
uniquely identify the sample buffer.
pdbx_buffer_components
Constituents of buffer in sample
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<PDBx:pdbx_buffer_componentsCategory>
<PDBx:pdbx_buffer_components buffer_id="1" id="1">
<PDBx:conc>4 </PDBx:conc>
<PDBx:details></PDBx:details>
<PDBx:name>NaCl</PDBx:name>
<PDBx:volume>0.200 </PDBx:volume>
</PDBx:pdbx_buffer_components>
<PDBx:pdbx_buffer_components buffer_id="1" id="2">
<PDBx:conc>100</PDBx:conc>
<PDBx:details></PDBx:details>
<PDBx:name>Acetic Acid</PDBx:name>
<PDBx:volume>0.047 </PDBx:volume>
</PDBx:pdbx_buffer_components>
<PDBx:pdbx_buffer_components buffer_id="1" id="3">
<PDBx:conc>neat</PDBx:conc>
<PDBx:details></PDBx:details>
<PDBx:name>water</PDBx:name>
<PDBx:volume>0.700 </PDBx:volume>
</PDBx:pdbx_buffer_components>
</PDBx:pdbx_buffer_componentsCategory>
0
1
0
1
0
1
0
1
0
1
0
1
1
1
pdbx_buffer_componentsCategory
This property indicates that datablock
has a category element pdbx_buffer_components.
pdbx_buffer_componentsItem
Abstract Datatype property for pdbx_buffer_components items.
reference_to_pdbx_buffer_components
cross-reference to pdbx_buffer_components
pdbx_buffer_components.conc
The millimolar concentration of buffer component.
200
%
mM
mg/mL
M
g/L
The concentration units of the component.
mg/mL for mg per milliliter
mM for millimolar
% for percent by volume
pdbx_buffer_components.details
Any additional details to do with buffer composition.
pH adjusted with NaOH
pdbx_buffer_components.isotopic_labeling
The isotopic composition of each component, including
the % labeling level, if known. For example:
1. Uniform (random) labeling with 15N: U-15N
2. Uniform (random) labeling with 13C, 15N at known labeling
levels: U-95% 13C;U-98% 15N
3. Residue selective labeling: U-95% 15N-Thymine
4. Site specific labeling: 95% 13C-Ala18,
5. Natural abundance labeling in an otherwise uniformly labled
biomolecule is designated by NA: U-13C; NA-K,H
U-15N
U-13C
U-15N,13C
U-2H
other
pdbx_buffer_components.name
The name of each buffer component.
Acetic acid
pdbx_buffer_components.volume
The volume of buffer component.
0.200
pdbx_buffer_components.buffer_id
This data item is a pointer to attribute id in category pdbx_buffer in the BUFFER category.
pdbx_buffer_components.id
The value of attribute id in category pdbx_buffer_components must
uniquely identify a component of the buffer.
pdbx_chem_comp_atom_edit
Data items in the PDBX_CHEM_COMP_ATOM_EDIT category provide
atom level editing instructions to be applied to imported
chemical components.
Example 1 -
<PDBx:pdbx_chem_comp_atom_editCategory>
<PDBx:pdbx_chem_comp_atom_edit ordinal="1">
<PDBx:atom_id>HN2</PDBx:atom_id>
<PDBx:comp_id>LYS</PDBx:comp_id>
<PDBx:edit_op>DELETE</PDBx:edit_op>
</PDBx:pdbx_chem_comp_atom_edit>
</PDBx:pdbx_chem_comp_atom_editCategory>
1
1
1
1
1
1
0
1
1
1
1
pdbx_chem_comp_atom_editCategory
This property indicates that datablock
has a category element pdbx_chem_comp_atom_edit.
pdbx_chem_comp_atom_editItem
Abstract Datatype property for pdbx_chem_comp_atom_edit items.
reference_to_pdbx_chem_comp_atom_edit
cross-reference to pdbx_chem_comp_atom_edit
pdbx_chem_comp_atom_edit.atom_id
The identifier for the target atom in imported component to be edited.
pdbx_chem_comp_atom_edit.comp_id
This data item is a pointer to attribute comp_id in category pdbx_chem_comp_import in the CHEM_COMP
category.
pdbx_chem_comp_atom_edit.edit_atom_id
The identifier for the edited atom in the generated component.
pdbx_chem_comp_atom_edit.edit_atom_value
The value for the edited atomic property value in the generated component.
RENAME
DELETE
ADD
CHARGE
PARTIAL_CHARGE
MODEL_CARTN_X
MODEL_CARTN_Y
MODEL_CARTN_Z
STEREO_CONFIG
AROMATIC_FLAG
The operation applied to the named imported component.
pdbx_chem_comp_atom_edit.ordinal
This data item uniquely identifies and orders each atom edit instruction.
pdbx_chem_comp_audit
Data items in the PDBX_CHEM_COMP_AUDIT category records
the status and tracking information for this component.
Example 1 -
<PDBx:pdbx_chem_comp_auditCategory>
<PDBx:pdbx_chem_comp_audit action_type="CREATE" comp_id="ATP" date="2007-12-01">
<PDBx:annotator>JY</PDBx:annotator>
</PDBx:pdbx_chem_comp_audit>
</PDBx:pdbx_chem_comp_auditCategory>
0
1
0
1
0
1
1
1
1
pdbx_chem_comp_auditCategory
This property indicates that datablock
has a category element pdbx_chem_comp_audit.
pdbx_chem_comp_auditItem
Abstract Datatype property for pdbx_chem_comp_audit items.
reference_to_pdbx_chem_comp_audit
cross-reference to pdbx_chem_comp_audit
pdbx_chem_comp_audit.annotator
The initials of the annotator creating of modifying the component.
JO
SJ
KB
pdbx_chem_comp_audit.details
Additional details decribing this change.
Added C14 as a leaving atom.
pdbx_chem_comp_audit.processing_site
An identifier for the wwPDB site creating or modifying the component.
RCSB
PDBE
PDBJ
BMRB
CREATE
CHANGE_STATUS
CHANGE_ATOM_NOMENCLATURE
CHANGE_MODEL
CHANGE_BOND
CHANGE_STEREO
CHANGE_DESCRIPTOR
CHANGE_NAME
OTHER
The action associated with this audit record.
pdbx_chem_comp_audit.comp_id
This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP
category.
pdbx_chem_comp_audit.date
The date associated with this audit record.
pdbx_chem_comp_bond_edit
Data items in the PDBX_CHEM_COMP_BOND_EDIT category provide
bond level editing instructions to be applied to imported
chemical components.
Example 1 -
<PDBx:pdbx_chem_comp_bond_editCategory>
<PDBx:pdbx_chem_comp_bond_edit atom_id_1="OXT" atom_id_2="HXT" comp_id="LYS" edit_op="DELETE">
<PDBx:ordinal>1</PDBx:ordinal>
</PDBx:pdbx_chem_comp_bond_edit>
</PDBx:pdbx_chem_comp_bond_editCategory>
0
1
1
1
1
1
1
1
pdbx_chem_comp_bond_editCategory
This property indicates that datablock
has a category element pdbx_chem_comp_bond_edit.
pdbx_chem_comp_bond_editItem
Abstract Datatype property for pdbx_chem_comp_bond_edit items.
reference_to_pdbx_chem_comp_bond_edit
cross-reference to pdbx_chem_comp_bond_edit
pdbx_chem_comp_bond_edit.edit_bond_value
The value for the edited bond property value in the generated component.
pdbx_chem_comp_bond_edit.ordinal
This data item uniquely identifies and orders each bond edit instruction.
pdbx_chem_comp_bond_edit.atom_id_1
The identifier for the first atom in the target bond
in imported component.
pdbx_chem_comp_bond_edit.atom_id_2
The identifier for the second atom in the target bond
in imported component.
pdbx_chem_comp_bond_edit.comp_id
This data item is a pointer to attribute comp_id in category pdbx_chem_comp_import in the CHEM_COMP
category.
DELETE
ADD
VALUE_ORDER
VALUE_DIST
STEREO_CONFIG
AROMATIC_FLAG
The operation or assignment applied to the named imported component.
pdbx_chem_comp_descriptor
Data items in the CHEM_COMP_DESCRIPTOR category provide
string descriptors of component chemical structure.
Example 1 -
<PDBx:pdbx_chem_comp_descriptorCategory>
<PDBx:pdbx_chem_comp_descriptor comp_id="ATP" program="OPENEYE" program_version="1.5.0" type="SMILES">
<PDBx:descriptor>c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N</PDBx:descriptor>
</PDBx:pdbx_chem_comp_descriptor>
</PDBx:pdbx_chem_comp_descriptorCategory>
1
1
0
1
1
1
1
1
pdbx_chem_comp_descriptorCategory
This property indicates that datablock
has a category element pdbx_chem_comp_descriptor.
pdbx_chem_comp_descriptorItem
Abstract Datatype property for pdbx_chem_comp_descriptor items.
reference_to_pdbx_chem_comp_descriptor
cross-reference to pdbx_chem_comp_descriptor
pdbx_chem_comp_descriptor.descriptor
This data item contains the descriptor value for this
component.
pdbx_chem_comp_descriptor.ordinal
Ordinal index for this category.
pdbx_chem_comp_descriptor.comp_id
This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP
category.
pdbx_chem_comp_descriptor.program
This data item contains the name of the program
or library used to compute the descriptor.
OpenEye OECHEM library
OPENEYE
CACTVS program library
CACTVS
Daylight program library
DAYLIGHT
Other program or library
OTHER
pdbx_chem_comp_descriptor.program_version
This data item contains the version of the program
or library used to compute the descriptor.
SMILES_CANNONICAL
SMILES_CANONICAL
SMILES
InChI
InChI_MAIN
InChI_MAIN_FORMULA
InChI_MAIN_CONNECT
InChI_MAIN_HATOM
InChI_CHARGE
InChI_STEREO
InChI_ISOTOPE
InChI_FIXEDH
InChI_RECONNECT
InChIKey
This data item contains the descriptor type.
pdbx_chem_comp_feature
Additional features associated with the chemical component.
Example 1 -
<PDBx:pdbx_chem_comp_featureCategory>
<PDBx:pdbx_chem_comp_feature comp_id="00X" source="PDB" type="ENZYME INHIBITED" value="ASPARTIC PROTEINASE"></PDBx:pdbx_chem_comp_feature>
<PDBx:pdbx_chem_comp_feature comp_id="00X" source="PDB" type="FUNCTION" value="Transistion-state analogue inhibitor"></PDBx:pdbx_chem_comp_feature>
<PDBx:pdbx_chem_comp_feature comp_id="00X" source="IUCR" type="STRUCTURE IMAGE URL" value="http://journals.iucr.org/00X.jpg"></PDBx:pdbx_chem_comp_feature>
</PDBx:pdbx_chem_comp_featureCategory>
0
1
1
1
1
1
pdbx_chem_comp_featureCategory
This property indicates that datablock
has a category element pdbx_chem_comp_feature.
pdbx_chem_comp_featureItem
Abstract Datatype property for pdbx_chem_comp_feature items.
reference_to_pdbx_chem_comp_feature
cross-reference to pdbx_chem_comp_feature
pdbx_chem_comp_feature.support
The supporting evidence for this feature.
Biological assay
Data obtained from PNAS August 17, 1999 vol. 96 no. 17 9586-9590
pdbx_chem_comp_feature.comp_id
The component identifier for this feature.
ABC
ATP
pdbx_chem_comp_feature.source
The information source for the component feature.
PDB
CHEBI
DRUGBANK
PUBCHEM
pdbx_chem_comp_feature.type
The component feature type.
FUNCTION
ENZYME INHIBITED
STRUCTURE IMAGE URL
pdbx_chem_comp_feature.value
The component feature value.
pdbx_chem_comp_identifier
Data items in the CHEM_COMP_IDENTIFIER category provide
identifiers for chemical components.
Example 1 -
<PDBx:pdbx_chem_comp_identifierCategory>
<PDBx:pdbx_chem_comp_identifier comp_id="ATP" program="ACDLabs" program_version="10.04" type="SYSTEMATIC NAME">
<PDBx:identifier>adenosine 5'-(tetrahydrogen triphosphate)</PDBx:identifier>
</PDBx:pdbx_chem_comp_identifier>
</PDBx:pdbx_chem_comp_identifierCategory>
1
1
0
1
1
1
1
1
pdbx_chem_comp_identifierCategory
This property indicates that datablock
has a category element pdbx_chem_comp_identifier.
pdbx_chem_comp_identifierItem
Abstract Datatype property for pdbx_chem_comp_identifier items.
reference_to_pdbx_chem_comp_identifier
cross-reference to pdbx_chem_comp_identifier
pdbx_chem_comp_identifier.identifier
This data item contains the identifier value for this
component.
pdbx_chem_comp_identifier.ordinal
Ordinal index for this category.
pdbx_chem_comp_identifier.comp_id
This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP
category.
pdbx_chem_comp_identifier.program
This data item contains the name of the program
or library used to compute the identifier.
OpenEye OECHEM program
OPENEYE
Daylight program library
DAYLIGHT
Advanced Chemistry Development Naming Program
ACD
Belstein AutoNom Naming Program
AUTONOM
Compound identifier
PUBCHEM_CID
Substance identifier
PUBCHEM_SID
Other program or library
OTHER
pdbx_chem_comp_identifier.program_version
This data item contains the version of the program
or library used to compute the identifier.
COMMON NAME
SYSTEMATIC NAME
CAS REGISTRY NUMBER
PUBCHEM Identifier
MDL Identifier
This data item contains the identifier type.
pdbx_chem_comp_import
Data items in the PDBX_CHEM_COMP_IMPORT category identify
existing chemical components to be imported into the
current component definition. Components in this list
can be edited by instructions in categories
pdbx_chem_comp_atom_edit and pdbx_chem_comp_bond_edit.
Example 1 -
<PDBx:pdbx_chem_comp_importCategory>
<PDBx:pdbx_chem_comp_import comp_id="ATP"></PDBx:pdbx_chem_comp_import>
</PDBx:pdbx_chem_comp_importCategory>
1
pdbx_chem_comp_importCategory
This property indicates that datablock
has a category element pdbx_chem_comp_import.
pdbx_chem_comp_importItem
Abstract Datatype property for pdbx_chem_comp_import items.
reference_to_pdbx_chem_comp_import
cross-reference to pdbx_chem_comp_import
pdbx_chem_comp_import.comp_id
This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP
category.
pdbx_construct
Data items in the PDBX_CONSTRUCT category specify a sequence of
nucleic acids or amino acids. It is a catch-all that may be used to
provide details of sequences known to be relevant to the project as well
as primers, plasmids, proteins and such like that are either used or
produced during the protein production process. Molecules described
here are not necessarily complete, so for instance it would be
possible to include either a complete plasmid or just its insert.
This category may be considered as an abbreviated form of _entity where
the molecules described are not required to appear in the final co-ordinates.
Note that the details provided here all pertain to a single entry as defined
at deposition. It is anticipated that attribute id in category pdbx_construct would also be
composed of a sequence that is unique within a given site prefixed by a code
that identifies that site and would, therefore, be GLOBALLY unique. Thus
this category could also be used locally to store details about the different
constructs used during protein production without reference to the entry_id
(which only becomes a meaningful concept during deposition).
Example 1 - hypothetical example
<PDBx:pdbx_constructCategory>
<PDBx:pdbx_construct id="1">
<PDBx:entity_id>1</PDBx:entity_id>
<PDBx:entry_id>111000111</PDBx:entry_id>
<PDBx:seq> gatgctgtag gcataggctt ggttatgccg gtactgccgg gcctcttgcg ggatatcgtc
gctcaaggcg cactcccgtt ctggataatg ttttttgcgc cgacatcata acggttctgg
caaatattct gaaatgagct gttgacaatt aatcatcgat aagcttcttg
# - - - - data truncated for brevity - - - -</PDBx:seq>
<PDBx:type>DNA</PDBx:type>
</PDBx:pdbx_construct>
</PDBx:pdbx_constructCategory>
0
1
0
1
0
1
0
1
1
1
1
1
1
1
0
1
1
1
1
1
1
pdbx_constructCategory
This property indicates that datablock
has a category element pdbx_construct.
pdbx_constructItem
Abstract Datatype property for pdbx_construct items.
reference_to_pdbx_construct
cross-reference to pdbx_construct
plasmid
protein
insert
primer
transcript
The primary function of the construct. This should be considered
as a guideline only.
pdbx_construct.date
The date that the sequence was determined.
2003-12-25
2003-12-25:09:00
pdbx_construct.details
Additional details about the construct that cannot be
represented in the category _pdbx_construct_feature.
pdbx_construct.entity_id
In cases where the construct IS found in the co-ordinates then this
item provides a pointer to attribute id in category entity in the ENTITY category for
the corresponding molecule.
pdbx_construct.entry_id
The value of attribute entry_id in category pdbx_construct uniquely identifies
a sample consisting of one or more proteins whose structure is
to be determined. This is a pointer to attribute id in category entry. This item may
be a site dependent bar code.
pdbx_construct.name
attribute name in category pdbx_construct provides a placeholder for the local name
of the construct, for example the plasmid name if this category
is used to list plasmids.
pdbx_construct.organisation
attribute organisation in category pdbx_construct describes the organisation in which
the attribute id in category pdbx_construct is unique. This will normally be the lab
in which the constrcut originated. It is envisaged that this item
will permit a globally unique identifier to be constructed in cases
where this is not possible from the attribute id in category pdbx_construct alone.
pdbx_construct.robot_id
In cases where the sequence has been determined by a robot this
data item provides a pointer to pdbx_robot_system.id in the
PDBX_ROBOT_SYSTEM category for the robot responsible
pdbx_construct.seq
sequence expressed as string of one-letter base codes or one
letter amino acid codes. Unusual residues may be represented
either using the appropriate one letter code wild cards or
by the three letter code in parentheses.
gatgctgtag gcataggctt ggttatgccg gtactgccgg gcctcttgcg ggatatcgtc
gctcaaggcg cactcccgtt ctggataatg ttttttgcgc cgacatcata acggttctgg
caaatattct gaaatgagct gttgacaatt aatcatcgat aagcttcttg
DNA
RNA
cDNA
mRNA
tRNA
protein
The type of nucleic acid sequence in the construct. Note that
to find all the DNA molecules it is necessary to search for
DNA + cDNA and for RNA, RNA + mRNA + tRNA.
pdbx_construct.id
The value of attribute id in category pdbx_construct must uniquely identify a record
in the PDBX_CONSTRUCT list and should be arranged so that it is
composed of a site-speicific prefix combined with a value that is
unique within a given site.Note that this item need not be a
number; it can be any unique identifier.
pdbx_construct_feature
Data items in the PDBX_CONSTRUCT_FEATURE category may be used to
specify various properties of a nucleic acid sequence used during
protein production.
Example 1 - vector pUC28
<PDBx:pdbx_construct_featureCategory>
<PDBx:pdbx_construct_feature construct_id="1" id="1">
<PDBx:details>pKK84-1 ClaI 5260bp 5247..5247 ptac11 TaqI-TaqI 192bp, -35 trp promoter -> pEA300 5452bp</PDBx:details>
<PDBx:end_seq></PDBx:end_seq>
<PDBx:entry_id>111000111</PDBx:entry_id>
<PDBx:start_seq></PDBx:start_seq>
<PDBx:type></PDBx:type>
</PDBx:pdbx_construct_feature>
<PDBx:pdbx_construct_feature construct_id="1" id="2">
<PDBx:details>pKK84-1 1..5246 5246bp ClaI = AT^CGAT TaqI = T^CGA cgact...</PDBx:details>
<PDBx:end_seq></PDBx:end_seq>
<PDBx:entry_id>111000111</PDBx:entry_id>
<PDBx:start_seq></PDBx:start_seq>
<PDBx:type></PDBx:type>
</PDBx:pdbx_construct_feature>
<PDBx:pdbx_construct_feature construct_id="1" id="3">
<PDBx:details>ptac11 190bp ...cat TaqI = T^CGA ClaI = AT^CGAT</PDBx:details>
<PDBx:end_seq>5436</PDBx:end_seq>
<PDBx:entry_id>111000111</PDBx:entry_id>
<PDBx:start_seq>5247</PDBx:start_seq>
<PDBx:type></PDBx:type>
</PDBx:pdbx_construct_feature>
<PDBx:pdbx_construct_feature construct_id="1" id="4">
<PDBx:details>pKK84-1 5247..5260 14bp</PDBx:details>
<PDBx:end_seq>5450</PDBx:end_seq>
<PDBx:entry_id>111000111</PDBx:entry_id>
<PDBx:start_seq>5437</PDBx:start_seq>
<PDBx:type></PDBx:type>
</PDBx:pdbx_construct_feature>
<PDBx:pdbx_construct_feature construct_id="1" id="5">
<PDBx:details>SIT unique EcoRI-ClaI-HindIII-BamHI-PvuII</PDBx:details>
<PDBx:end_seq></PDBx:end_seq>
<PDBx:entry_id>111000111</PDBx:entry_id>
<PDBx:start_seq></PDBx:start_seq>
<PDBx:type>misc_binding</PDBx:type>
</PDBx:pdbx_construct_feature>
<PDBx:pdbx_construct_feature construct_id="1" id="6">
<PDBx:details>ORI E. coli pMB1 (ColE1 and pBR322)</PDBx:details>
<PDBx:end_seq></PDBx:end_seq>
<PDBx:entry_id>111000111</PDBx:entry_id>
<PDBx:start_seq></PDBx:start_seq>
<PDBx:type>rep_origin</PDBx:type>
</PDBx:pdbx_construct_feature>
<PDBx:pdbx_construct_feature construct_id="1" id="7">
<PDBx:details>PRO E. coli trp</PDBx:details>
<PDBx:end_seq></PDBx:end_seq>
<PDBx:entry_id>111000111</PDBx:entry_id>
<PDBx:start_seq></PDBx:start_seq>
<PDBx:type>promoter</PDBx:type>
</PDBx:pdbx_construct_feature>
<PDBx:pdbx_construct_feature construct_id="1" id="8">
<PDBx:details>ANT E. coli beta-lactamase gene (bla) ampicillin resistance gene (apr/amp)</PDBx:details>
<PDBx:end_seq></PDBx:end_seq>
<PDBx:entry_id>111000111</PDBx:entry_id>
<PDBx:start_seq></PDBx:start_seq>
<PDBx:type>CDS</PDBx:type>
</PDBx:pdbx_construct_feature>
</PDBx:pdbx_construct_featureCategory>
0
1
0
1
1
1
0
1
0
1
1
1
pdbx_construct_featureCategory
This property indicates that datablock
has a category element pdbx_construct_feature.
pdbx_construct_featureItem
Abstract Datatype property for pdbx_construct_feature items.
reference_to_pdbx_construct_feature
cross-reference to pdbx_construct_feature
pdbx_construct_feature.details
Details that describe the feature
pdbx_construct_feature.end_seq
The sequence position at which the feature ends
pdbx_construct_feature.entry_id
The value of attribute entry_id in category pdbx_construct_feature uniquely identifies
a sample consisting of one or more proteins whose structure is
to be determined. This is a pointer to attribute id in category entry. This item may
be a site dependent bar code.
pdbx_construct_feature.start_seq
The sequence position at which the feature begins
pdbx_construct_feature.type
The type of the feature
pdbx_construct_feature.construct_id
The value of attribute construct_id in category pdbx_construct_feature uniquely
identifies the construct with which the feature is
associated. This is a pointer to attribute id
in category pdbx_construct This item may be a site dependent bar code.
pdbx_construct_feature.id
The value of attribute id in category pdbx_construct_feature must uniquely
identify a record in the PDBX_CONSTRUCT_FEATURE list.
Note that this item need not be a number; it can be any unique
identifier.
pdbx_contact_author
Data items in the PDBX_CONTACT_AUTHOR category record details
about the name and address of the author to be contacted
concerning the contents of this data block. This category atomizes
information to a greater degree than the standard AUDIT_CONTACT_AUTHOR
category.
Example 1 -
<PDBx:pdbx_contact_authorCategory>
<PDBx:pdbx_contact_author id="1">
<PDBx:address_1>Department of Biophysical Chemistry</PDBx:address_1>
<PDBx:address_2>Merck Research Laboratories</PDBx:address_2>
<PDBx:address_3>P. O. Box 2000, Ry80M203</PDBx:address_3>
<PDBx:city>Rahway</PDBx:city>
<PDBx:country>UNITED STATES</PDBx:country>
<PDBx:email>paula_fitzgerald@merck.com</PDBx:email>
<PDBx:fax>908 594 6645</PDBx:fax>
<PDBx:name_first>Paula</PDBx:name_first>
<PDBx:name_last>Fitzgerald</PDBx:name_last>
<PDBx:name_mi>M.D.</PDBx:name_mi>
<PDBx:name_salutation>Dr.</PDBx:name_salutation>
<PDBx:organization_type>commercial</PDBx:organization_type>
<PDBx:phone>908 594 5510</PDBx:phone>
<PDBx:postal_code>07065</PDBx:postal_code>
<PDBx:role>principal investigator/group leader</PDBx:role>
<PDBx:state_province>New Jersey</PDBx:state_province>
</PDBx:pdbx_contact_author>
</PDBx:pdbx_contact_authorCategory>
0
1
0
1
0
1
0
1
1
1
1
1
0
1
0
1
1
1
1
1
1
1
1
1
0
1
0
1
0
1
0
1
0
1
1
pdbx_contact_authorCategory
This property indicates that datablock
has a category element pdbx_contact_author.
pdbx_contact_authorItem
Abstract Datatype property for pdbx_contact_author items.
reference_to_pdbx_contact_author
cross-reference to pdbx_contact_author
pdbx_contact_author.address_1
The mailing address of the author of the data block to whom
correspondence should be addressed, line 1 of 3.
610 Taylor Road
pdbx_contact_author.address_2
The mailing address of the author of the data block to whom
correspondence should be addressed, line 2 of 3.
Department of Chemistry and Chemical Biology
pdbx_contact_author.address_3
The mailing address of the author of the data block to whom
correspondence should be addressed, line 3 of 3.
Busch Campus
pdbx_contact_author.city
The mailing address of the author of the data block to whom
correspondence should be addressed, city.
Piscataway
AFRICA
ANTARTICA
ASIA
AUSTRALIA
EUROPE
NORTH AMERICA
SOUTH AMERICA
The continent of the author of the data block to whom
correspondence should be addressed.
AFRICA
ANTARTICA
ASIA
AUSTRALIA
EUROPE
NORTH AMERICA
SOUTH AMERICA
pdbx_contact_author.country
The country of the author of the data block to whom
correspondence should be addressed.
UNITED STATES
UNITED KINGDOM
AUSTRALIA
pdbx_contact_author.email
The electronic mail address of the author of the data block to
whom correspondence should be addressed, in a form recognisable
to international networks.
name@host.domain.country
bm@iucr.ac.uk
pdbx_contact_author.fax
The facsimile telephone number of the author of the data
block to whom correspondence should be addressed.
The recommended style includes the international dialing
prefix, the area code in parentheses, followed by the
local number with no spaces.
12(34) 947 7334
732 445 0103
pdbx_contact_author.name_first
The first name of the author of the data block to whom correspondence
should be addressed.
Percival
Loyd
Susan
pdbx_contact_author.name_last
The last name of the author of the data block to whom correspondence
should be addressed.
Samuels
Rodgers
pdbx_contact_author.name_mi
The middle initial(s) of the author of the data block to whom correspondence
should be addressed.
T.
M.F.
Dr.
Prof.
Mr.
Ms.
Mrs.
The salutation of the author of the data block to whom correspondence
should be addressed.
Dr.
Prof.
Mr.
Ms.
Mrs.
academic
commercial
government
other
The organization type to which this author is affiliated.
academic
commercial
government
other
pdbx_contact_author.phone
The telephone number of the author of the data block to whom
correspondence should be addressed.
The recommended style includes the international dialing
prefix, the area code in parentheses, followed by the
local number and any extension number prefixed by 'x',
with no spaces. The earlier convention of including
the international dialing prefixes in parentheses is no longer
recommended.
12 (34) 947 7330
947 732 0103 x8320
pdbx_contact_author.postal_code
The mailing address of the author of the data block to whom
correspondence should be addressed, zip code.
08854
principal investigator/group leader
responsible scientist
investigator
The role of this author in the project depositing this data.
principal investigator/group leader
responsible scientist
investigator
pdbx_contact_author.state_province
The mailing address of the author of the data block to whom
correspondence should be addressed, state or province.
New Jersey
1
2
3
4
5
6
7
8
9
10
A unique integer identifier for this author
1 2 3
pdbx_coordinate_model
The details of the composition of the coordinate model.
Example 1 -
<PDBx:pdbx_coordinate_modelCategory>
<PDBx:pdbx_coordinate_model asym_id="A">
<PDBx:type>C-ALPHA ONLY</PDBx:type>
</PDBx:pdbx_coordinate_model>
<PDBx:pdbx_coordinate_model asym_id="B">
<PDBx:type>C-APLHA ONLY</PDBx:type>
</PDBx:pdbx_coordinate_model>
<PDBx:pdbx_coordinate_model asym_id="X">
<PDBx:type>P ONLY</PDBx:type>
</PDBx:pdbx_coordinate_model>
<PDBx:pdbx_coordinate_model asym_id="Y">
<PDBx:type>P ONLY</PDBx:type>
</PDBx:pdbx_coordinate_model>
</PDBx:pdbx_coordinate_modelCategory>
1
1
1
pdbx_coordinate_modelCategory
This property indicates that datablock
has a category element pdbx_coordinate_model.
pdbx_coordinate_modelItem
Abstract Datatype property for pdbx_coordinate_model items.
reference_to_pdbx_coordinate_model
cross-reference to pdbx_coordinate_model
C-ALPHA ONLY
P ONLY
A classification of the composition of the coordinate model.
C-ALPHA ONLY
P ONLY
pdbx_coordinate_model.asym_id
A reference to attribute id in category struct_asym.
1
A
pdbx_database_PDB_obs_spr
The PDBX_DATABASE_PDB_OBS_SPR category provides placeholders
for information on obsolete/superseded PDB entries
1
1
1
1
1
1
pdbx_database_PDB_obs_sprCategory
This property indicates that datablock
has a category element pdbx_database_PDB_obs_spr.
pdbx_database_PDB_obs_sprItem
Abstract Datatype property for pdbx_database_PDB_obs_spr items.
reference_to_pdbx_database_PDB_obs_spr
cross-reference to pdbx_database_PDB_obs_spr
pdbx_database_PDB_obs_spr.date
The date of replacement.
1997-03-30
OBSLTE
SPRSDE
Identifier for the type of obsolete entry to be added to this entry.
OBSLTE
pdbx_database_PDB_obs_spr.pdb_id
The new PDB identifier for the replaced entry.
2ABC
pdbx_database_PDB_obs_spr.replace_pdb_id
The PDB identifier for the replaced (OLD) entry/entries.
3ABC
pdbx_database_message
The PDBX_DATABASE_MESSAGE category provides information about
correspondance related to a structure deposition.
1
1
1
1
0
1
1
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
pdbx_database_messageCategory
This property indicates that datablock
has a category element pdbx_database_message.
pdbx_database_messageItem
Abstract Datatype property for pdbx_database_message items.
reference_to_pdbx_database_message
cross-reference to pdbx_database_message
DEPOSIT
REMINDER
QUERY
OTHER
This code defines the content of the message.
pdbx_database_message.date
This is the date when a message was sent or received.
pdbx_database_message.message
The text of the message.
FAX
EMAIL
MAIL
PHONE
Defines how the message was sent or received.
pdbx_database_message.receiver
The name of the receiver.
pdbx_database_message.receiver_address_email
The email address of the receiver.
pdbx_database_message.receiver_address_fax
The FAX phone number of the receiver.
pdbx_database_message.receiver_address_mail
The postal address of the receiver.
pdbx_database_message.receiver_address_phone
The phone number of the receiver.
pdbx_database_message.sender
The name of the sender.
pdbx_database_message.sender_address_email
The email address of the sender.
pdbx_database_message.sender_address_fax
The FAX phone number of the sender.
pdbx_database_message.sender_address_mail
The postal address of the sender.
pdbx_database_message.sender_address_phone
The phone number of the sender.
pdbx_database_message.entry_id
The value of attribute entry_id in category pdbx_database_message identifies the data block.
BDL001
pdbx_database_message.message_id
This is an unique and sequential identifier for a message.
message 1
pdbx_database_proc
Internal records to track the data processing cycle.
<PDBx:pdbx_database_procCategory>
<PDBx:pdbx_database_proc cycle_id="1" entry_id="BDL001">
<PDBx:date_begin_cycle>1998-02-27</PDBx:date_begin_cycle>
<PDBx:date_end_cycle>1998-02-27</PDBx:date_end_cycle>
</PDBx:pdbx_database_proc>
</PDBx:pdbx_database_procCategory>
1
1
1
1
0
1
1
1
pdbx_database_procCategory
This property indicates that datablock
has a category element pdbx_database_proc.
pdbx_database_procItem
Abstract Datatype property for pdbx_database_proc items.
reference_to_pdbx_database_proc
cross-reference to pdbx_database_proc
pdbx_database_proc.date_begin_cycle
This is the date of the start of the processing cycle.
1983-02-27
pdbx_database_proc.date_end_cycle
This is the date of the end of the processing cycle.
1983-02-27
pdbx_database_proc.details
Special details about the current processing cycle.
pdbx_database_proc.cycle_id
This is a number of the processing cycle.
1 for the initial cycle
pdbx_database_proc.entry_id
The value of attribute entry_id in category pdbx_database_proc identifies the data block.
BDL001
pdbx_database_related
Data items in PDBX_DATABASE_RELATED contain references to entries
that are related to the this entry.
<PDBx:pdbx_database_relatedCategory>
<PDBx:pdbx_database_related content_type="native structure" db_id="1ABC" db_name="PDB"></PDBx:pdbx_database_related>
</PDBx:pdbx_database_relatedCategory>
0
1
1
1
1
pdbx_database_relatedCategory
This property indicates that datablock
has a category element pdbx_database_related.
pdbx_database_relatedItem
Abstract Datatype property for pdbx_database_related items.
reference_to_pdbx_database_related
cross-reference to pdbx_database_related
pdbx_database_related.details
A description of the related entry.
1ABC contains the same protein complexed with Netropsin.
minimized average structure
representative structure
ensemble
derivative structure
native structure
associated EM volume
associated NMR restraints
associated structure factors
protein target sequence and/or protocol data
split
re-refinement
unspecified
other
q
The identifying content type of the related entry.
minimized average structure
representative structure
ensemble
derivative structure
native structure
associated EM volume
associated NMR restraints
associated structure factors
protein target sequence and/or protocol data
split
re-refinement
unspecified
other
pdbx_database_related.db_id
The identifying code in the related database.
1ABC
BDL001
pdbx_database_related.db_name
The name of the database containing the related entry.
PDB - Protein Databank
NDB - Nucleic Acid Database
BMRB - BioMagResBank
EMDB - Electron Microscopy Database
BMCD - Biological Macromolecule Crystallization Database
TARGETDB - Target Registration Database
PEPCDB - Protein Expression Purification and Crystalization Database
pdbx_database_remark
Data items in the PDBX_DATABASE_REMARK category record keep additional
information about the entry. They are mostly used to create
'non-standard' PDB REMARK annotations (6-99).
Example 1 - based on PDB entry 1ABC
<PDBx:pdbx_database_remarkCategory>
<PDBx:pdbx_database_remark id="1">
<PDBx:text> THE NON-CRYSTALLOGRAPHIC RELATIONSHIP BETWEEN THE THREE
DOUBLE HELICES IN THE ASYMMETRIC UNIT IS DESCRIBED
IN THE MTRIX1-3 RECORDS.</PDBx:text>
</PDBx:pdbx_database_remark>
</PDBx:pdbx_database_remarkCategory>
0
1
1
pdbx_database_remarkCategory
This property indicates that datablock
has a category element pdbx_database_remark.
pdbx_database_remarkItem
Abstract Datatype property for pdbx_database_remark items.
reference_to_pdbx_database_remark
cross-reference to pdbx_database_remark
pdbx_database_remark.text
The full text of the PDB remark record.
pdbx_database_remark.id
A unique identifier for the PDB remark record.
pdbx_database_status
These are internal RCSB records to keep track of data processing
and status of the entry.
<PDBx:pdbx_database_statusCategory>
<PDBx:pdbx_database_status entry_id="1ABC">
<PDBx:deposit_site>RCSB</PDBx:deposit_site>
<PDBx:process_site>RCSB</PDBx:process_site>
<PDBx:status_code>REL</PDBx:status_code>
</PDBx:pdbx_database_status>
</PDBx:pdbx_database_statusCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
0
1
0
1
1
pdbx_database_statusCategory
This property indicates that datablock
has a category element pdbx_database_status.
pdbx_database_statusItem
Abstract Datatype property for pdbx_database_status items.
reference_to_pdbx_database_status
cross-reference to pdbx_database_status
Y
N
This code indicates whether the entry belongs to
Structural Genomics Project.
Y
implicit
explicit
This code indicates whether the author's approval for
an entry was received explicitly or implicitly. The
latter is automatically implied by failure to respond
to the validation summary within the prescribed period.
implicit = automatic approval by failure to acknowledge
explicit = approval via depositor acknowledgement
REL
HOLD
HPUB
OBS
WDRN
The release status authorized by the depositor.
REL = Release
HOLD = On hold until yyyy-mm-dd
HPUB = On hold until publication
OBS = Entry has been obsoleted and replaced by another entry
WDRN = Entry has been withdrawn by depositor
pdbx_database_status.date_author_approval
The date the author's approval is received.
1983-02-20
pdbx_database_status.date_coordinates
The date the coordinates are received.
1983-02-21
pdbx_database_status.date_deposition_form
The date the deposition form is received.
1982-02-21
pdbx_database_status.date_hold_coordinates
At an author's request, a coordinate entry may be held after
processing for some period of time.
1983-02-28
pdbx_database_status.date_hold_nmr_constraints
At an author's request, the NMR constraint data may be held after
processing for some period of time.
1983-02-28
pdbx_database_status.date_hold_struct_fact
At an author's request, the structure factors may be held after
processing for some period of time.
1983-02-28
pdbx_database_status.date_manuscript
The date the manuscript is received.
1983-02-28
pdbx_database_status.date_nmr_constraints
The date the structure factors are received.
1983-02-28
pdbx_database_status.date_of_PDB_release
PDB release date. This is the date that appears in the PDB
REVDAT record.
1983-02-28
pdbx_database_status.date_of_mr_release
The date of PDB/RCSB release. This corresponds to the date
at which the entry is placed into the public archive.
1999-02-28
pdbx_database_status.date_of_sf_release
The date of PDB/RCSB release. This corresponds to the date
at which the entry is placed into the public archive.
1999-02-28
pdbx_database_status.date_struct_fact
The date the structure factors are received.
1983-02-28
pdbx_database_status.date_submitted
The date of complete deposition. This corresponds to the date
at which the PDB identifier is assigned.
1983-02-20
RELEASE NOW
HOLD FOR PUBLICATION
HOLD FOR 4 WEEKS
HOLD FOR 6 WEEKS
HOLD FOR 8 WEEKS
HOLD FOR 6 MONTHS
HOLD FOR 1 YEAR
The deposited coordinates for this deposition will be released according
the value of this item.
RELEASE NOW = Release immediately
HOLD FOR PUBLICATION = Hold until the primary citation is published
HOLD FOR 4 WEEKS = Hold for 4 weeks
HOLD FOR 6 WEEKS = Hold for 6 weeks
HOLD FOR 8 WEEKS = Hold for 8 weeks
HOLD FOR 6 MONTHS = Hold for 6 months
HOLD FOR 1 YEAR = Hold for 1 year
pdbx_database_status.dep_release_code_nmr_constraints
The deposited NMR constrait data for this deposition will be released according
the value of this item.
RELEASE NOW = Release immediately
HOLD FOR PUBLICATION = Hold until the primary citation is published
HOLD FOR 6 WEEKS = Hold for 6 weeks
HOLD FOR 6 MONTHS = Hold for 6 months
HOLD FOR 1 YEAR = Hold for 1 year
RELEASE NOW
HOLD FOR RELEASE
The sequence information for this deposition will be released according
the value of this item. Setting this status code to "RELEASE NOW" indicates
that the macromolecular sequence(s) for this entry may be displayed in PDB
status reports prior to the release of the entry. Setting this status
code to "HOLD FOR RELEASE" conceals the sequence information in PDB status
reports until the coordinate data for this entry are released.
RELEASE NOW = Release sequence information in status reports immediately
HOLD FOR RELEASE = Conceal sequence information in status reports until
coordinate data is release
pdbx_database_status.dep_release_code_struct_fact
The deposited structure factors for this deposition will be released according
the value of this item.
RELEASE NOW = Release immediately
HOLD FOR PUBLICATION = Hold until the primary citation is published
HOLD FOR 4 WEEKS = Hold for 4 weeks
HOLD FOR 6 WEEKS = Hold for 6 weeks
HOLD FOR 6 MONTHS = Hold for 6 months
HOLD FOR 1 YEAR = Hold for 1 year
NDB
RCSB
PDB
EBI
OSAKA
BMRB
BNL
The site where the file was deposited.
NDB
RCSB
PDB
EBI
OSAKA
BMRB
BNL
Y
N
At an author's request, an entry is to be held until
publication.
Y
pdbx_database_status.name_depositor
The last name of the depositor to be used in correspondance.
Smith
pdbx_database_status.pdb_date_of_author_approval
This is the date when PDB received the author's approval for an
entry which has been processed by NDB. (This is a place holder
for entries processed before Jan. 1, 1996.)
1983-02-27
NDB
RCSB
EBI
OSAKA
PDB
PRAGUE
The site where the file was deposited.
NDB
RCSB
EBI
OSAKA
PDB
PRAGUE
pdbx_database_status.rcsb_annotator
The initials of the annotator processing this entry.
BS
SJ
KB
Y
N
This code indicates whether the author's approval for
an entry has been received.
Y
Y
N
This code indicates whether the coordinates for an entry
have been received.
Y
Y
N
This code indicates whether the deposition form for an entry
has been received.
Y
pdbx_database_status.recvd_initial_deposition_date
The date of initial deposition. (The first message for
deposition has been received.)
1983-02-21
Y
N
This code indicates whether the internal approval for an entry
have been received.
Y
Y
N
This code indicates whether the manuscript for an entry
has been received.
Y
Y
N
This code indicates whether the NMR contraint data for an entry
have been received.
Y
Y
N
This code indicates whether the structure factors for an entry
have been received.
Y
PROC
WAIT
REL
HOLD
HPUB
OBS
WDRN
AUTH
POLC
REPL
DEL
REV
UPD
BIB
Code for status of file.
REL
HPUB
PROC
WAIT
REL
HOLD
HPUB
OBS
WDRN
AUTH
POLC
REPL
Code for status of NMR constraints file.
PROC = To be processed
REL = Release
HOLD = On hold until yyyy-mm-dd
HPUB = On hold until publication
OBS = Entry has been obsoleted and replaced by another entry
WDRN = Entry has been withdrawn by depositor
WAIT = Awaiting author approval
PROC
WAIT
REL
HOLD
HPUB
OBS
WDRN
AUTH
POLC
REPL
Code for status of structure factor file.
PROC = To be processed
REL = Released
HOLD = On hold until yyyy-mm-dd
HPUB = On hold until publication
OBS = Entry has been obsoleted and replaced by another entry
WDRN = Entry has been withdrawn by depositor
WAIT = Awaiting author approval
pdbx_database_status.entry_id
The value of attribute entry_id in category pdbx_database_status identifies the data block.
BDL001
pdbx_diffrn_reflns_shell
Data items in the DIFFRN_REFLNS_SHELL category record details about
the reflection data set within shells of resolution.
Example 1 - diffraction properties with shells
<PDBx:pdbx_diffrn_reflns_shellCategory>
<PDBx:pdbx_diffrn_reflns_shell d_res_high="5.18" d_res_low="50.00" diffrn_id="1">
<PDBx:Rmerge_I_obs>0.029</PDBx:Rmerge_I_obs>
<PDBx:chi_squared>1.154</PDBx:chi_squared>
<PDBx:number_obs>11791</PDBx:number_obs>
<PDBx:percent_possible_obs>100.000</PDBx:percent_possible_obs>
</PDBx:pdbx_diffrn_reflns_shell>
<PDBx:pdbx_diffrn_reflns_shell d_res_high="4.11" d_res_low="5.18" diffrn_id="1">
<PDBx:Rmerge_I_obs>0.033</PDBx:Rmerge_I_obs>
<PDBx:chi_squared>1.098</PDBx:chi_squared>
<PDBx:number_obs>11717</PDBx:number_obs>
<PDBx:percent_possible_obs>100.000</PDBx:percent_possible_obs>
</PDBx:pdbx_diffrn_reflns_shell>
<PDBx:pdbx_diffrn_reflns_shell d_res_high="3.59" d_res_low="4.11" diffrn_id="1">
<PDBx:Rmerge_I_obs>0.043</PDBx:Rmerge_I_obs>
<PDBx:chi_squared>1.044</PDBx:chi_squared>
<PDBx:number_obs>11792</PDBx:number_obs>
<PDBx:percent_possible_obs>100.000</PDBx:percent_possible_obs>
</PDBx:pdbx_diffrn_reflns_shell>
<PDBx:pdbx_diffrn_reflns_shell d_res_high="3.26" d_res_low="3.59" diffrn_id="1">
<PDBx:Rmerge_I_obs>0.059</PDBx:Rmerge_I_obs>
<PDBx:chi_squared>1.104</PDBx:chi_squared>
<PDBx:number_obs>11718</PDBx:number_obs>
<PDBx:percent_possible_obs>100.000</PDBx:percent_possible_obs>
</PDBx:pdbx_diffrn_reflns_shell>
<PDBx:pdbx_diffrn_reflns_shell d_res_high="3.03" d_res_low="3.26" diffrn_id="1">
<PDBx:Rmerge_I_obs>0.087</PDBx:Rmerge_I_obs>
<PDBx:chi_squared>1.160</PDBx:chi_squared>
<PDBx:number_obs>11753</PDBx:number_obs>
<PDBx:percent_possible_obs>100.000</PDBx:percent_possible_obs>
</PDBx:pdbx_diffrn_reflns_shell>
<PDBx:pdbx_diffrn_reflns_shell d_res_high="2.85" d_res_low="3.03" diffrn_id="1">
<PDBx:Rmerge_I_obs>0.130</PDBx:Rmerge_I_obs>
<PDBx:chi_squared>1.169</PDBx:chi_squared>
<PDBx:number_obs>11811</PDBx:number_obs>
<PDBx:percent_possible_obs>100.000</PDBx:percent_possible_obs>
</PDBx:pdbx_diffrn_reflns_shell>
<PDBx:pdbx_diffrn_reflns_shell d_res_high="2.71" d_res_low="2.85" diffrn_id="1">
<PDBx:Rmerge_I_obs>0.174</PDBx:Rmerge_I_obs>
<PDBx:chi_squared>1.170</PDBx:chi_squared>
<PDBx:number_obs>11752</PDBx:number_obs>
<PDBx:percent_possible_obs>100.000</PDBx:percent_possible_obs>
</PDBx:pdbx_diffrn_reflns_shell>
<PDBx:pdbx_diffrn_reflns_shell d_res_high="2.59" d_res_low="2.71" diffrn_id="1">
<PDBx:Rmerge_I_obs>0.227</PDBx:Rmerge_I_obs>
<PDBx:chi_squared>1.165</PDBx:chi_squared>
<PDBx:number_obs>11767</PDBx:number_obs>
<PDBx:percent_possible_obs>100.000</PDBx:percent_possible_obs>
</PDBx:pdbx_diffrn_reflns_shell>
</PDBx:pdbx_diffrn_reflns_shellCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
pdbx_diffrn_reflns_shellCategory
This property indicates that datablock
has a category element pdbx_diffrn_reflns_shell.
pdbx_diffrn_reflns_shellItem
Abstract Datatype property for pdbx_diffrn_reflns_shell items.
reference_to_pdbx_diffrn_reflns_shell
cross-reference to pdbx_diffrn_reflns_shell
pdbx_diffrn_reflns_shell.Rmerge_I_obs
The R factor for the reflections that satisfy the merging
criteria for the resolution shell.
pdbx_diffrn_reflns_shell.Rsym_value
The R factor for averaging the symmetry related reflections
for the resolution shell.
pdbx_diffrn_reflns_shell.chi_squared
The overall Chi-squared statistic for the resolution shell.
pdbx_diffrn_reflns_shell.number_obs
The number of observed reflections in the resolution shell.
pdbx_diffrn_reflns_shell.percent_possible_obs
The percentage of geometrically possible reflections represented
by reflections that satisfy the resolution limits established
by attribute d_resolution_high in category diffrn_reflns_shell and
attribute d_resolution_low in category diffrn_reflns_shell and the observation limit
established by attribute observed_criterion.
in category diffrn_reflns
pdbx_diffrn_reflns_shell.redundancy
The overall redundancy for the resolution shell.
pdbx_diffrn_reflns_shell.rejects
The number of rejected reflections in the resolution shell
pdbx_diffrn_reflns_shell.d_res_high
The highest resolution for the interplanar spacings in the
resolution shell.
pdbx_diffrn_reflns_shell.d_res_low
The lowest resolution for the interplanar spacings in the
resolution shell.
pdbx_diffrn_reflns_shell.diffrn_id
This data item is a pointer to attribute id in category diffrn in the DIFFRN category.
This item distingush the different data sets
pdbx_domain
Data items in the PDBX_DOMAIN category record information
about domain definitions.
A domain need not correspond to a completely polypeptide chain;
it can be composed of one or more segments in a single chain,
or by segments from more than one chain.
Example 1 -
<PDBx:pdbx_domainCategory>
<PDBx:pdbx_domain id="d1">
<PDBx:details>Chains A, B</PDBx:details>
</PDBx:pdbx_domain>
<PDBx:pdbx_domain id="d2">
<PDBx:details>Asym_id D Residues 1-134</PDBx:details>
</PDBx:pdbx_domain>
</PDBx:pdbx_domainCategory>
0
1
1
pdbx_domainCategory
This property indicates that datablock
has a category element pdbx_domain.
pdbx_domainItem
Abstract Datatype property for pdbx_domain items.
reference_to_pdbx_domain
cross-reference to pdbx_domain
pdbx_domain.details
A description of special aspects of the structural elements that
comprise a domain.
The loop between residues 18 and 23.
pdbx_domain.id
The value of attribute id in category pdbx_domain must uniquely identify a
record in the PDBX_DOMAIN list.
Note that this item need not be a number; it can be any unique
identifier.
pdbx_domain_range
Data items in the PDBX_DOMAIN_RANGE category identify the
beginning and ending points of polypeptide chain segments
that form all or part of a domain.
Example 1 -
<PDBx:pdbx_domain_rangeCategory>
<PDBx:pdbx_domain_range beg_label_alt_id="A" beg_label_asym_id="A" beg_label_comp_id="PRO" beg_label_seq_id="1" domain_id="d1" end_label_alt_id="A" end_label_asym_id="A" end_label_comp_id="GLY" end_label_seq_id="29"></PDBx:pdbx_domain_range>
<PDBx:pdbx_domain_range beg_label_alt_id="A" beg_label_asym_id="B" beg_label_comp_id="PRO" beg_label_seq_id="31" domain_id="d1" end_label_alt_id="A" end_label_asym_id="B" end_label_comp_id="GLY" end_label_seq_id="59"></PDBx:pdbx_domain_range>
<PDBx:pdbx_domain_range beg_label_alt_id="A" beg_label_asym_id="C" beg_label_comp_id="PRO" beg_label_seq_id="61" domain_id="d1" end_label_alt_id="A" end_label_asym_id="B" end_label_comp_id="GLY" end_label_seq_id="89"></PDBx:pdbx_domain_range>
<PDBx:pdbx_domain_range beg_label_alt_id="A" beg_label_asym_id="D" beg_label_comp_id="PRO" beg_label_seq_id="91" domain_id="d2" end_label_alt_id="A" end_label_asym_id="D" end_label_comp_id="GLY" end_label_seq_id="119"></PDBx:pdbx_domain_range>
<PDBx:pdbx_domain_range beg_label_alt_id="A" beg_label_asym_id="E" beg_label_comp_id="PRO" beg_label_seq_id="121" domain_id="d2" end_label_alt_id="A" end_label_asym_id="E" end_label_comp_id="GLY" end_label_seq_id="149"></PDBx:pdbx_domain_range>
<PDBx:pdbx_domain_range beg_label_alt_id="A" beg_label_asym_id="F" beg_label_comp_id="PRO" beg_label_seq_id="151" domain_id="d2" end_label_alt_id="A" end_label_asym_id="F" end_label_comp_id="GLY" end_label_seq_id="179"></PDBx:pdbx_domain_range>
</PDBx:pdbx_domain_rangeCategory>
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
1
1
1
1
1
pdbx_domain_rangeCategory
This property indicates that datablock
has a category element pdbx_domain_range.
pdbx_domain_rangeItem
Abstract Datatype property for pdbx_domain_range items.
reference_to_pdbx_domain_range
cross-reference to pdbx_domain_range
pdbx_domain_range.beg_auth_asym_id
A component of the identifier for the monomer at which this
segment of the domain begins.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_domain_range.beg_auth_comp_id
A component of the identifier for the monomer at which this
segment of the domain begins.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_domain_range.beg_auth_seq_id
A component of the identifier for the monomer at which this
segment of the domain begins.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_domain_range.end_auth_asym_id
A component of the identifier for the monomer at which this
segment of the domain ends.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_domain_range.end_auth_comp_id
A component of the identifier for the monomer at which this
segment of the domain ends.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_domain_range.end_auth_seq_id
A component of the identifier for the monomer at which this
segment of the domain ends.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_domain_range.beg_label_alt_id
A component of the identifier for the monomer at which this
segment of the domain begins.
This data item is a pointer to attribute id in category atom_sites_alt in the
ATOM_SITES_ALT category.
pdbx_domain_range.beg_label_asym_id
A component of the identifier for the monomer at which this
segment of the domain begins.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_domain_range.beg_label_comp_id
A component of the identifier for the monomer at which this
segment of the domain begins.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_domain_range.beg_label_seq_id
A component of the identifier for the monomer at which this
segment of the domain begins.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_domain_range.domain_id
This data item is a pointer to attribute id in category pdbx_domain in the
PDBX_DOMAIN category.
pdbx_domain_range.end_label_alt_id
A component of the identifier for the monomer at which this
segment of the domain ends.
This data item is a pointer to attribute id in category atom_sites_alt in the
ATOM_SITES_ALT category.
pdbx_domain_range.end_label_asym_id
A component of the identifier for the monomer at which this
segment of the domain ends.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_domain_range.end_label_comp_id
A component of the identifier for the monomer at which this
segment of the domain ends.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_domain_range.end_label_seq_id
A component of the identifier for the monomer at which this
segment of the domain ends.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_entity_assembly
The PDBX_ENTITY_ASSEMBLY category provides a chemical description
of the biological assembly studied in terms of its constituent
entities.
A complex composed of one copy of entities 1 and 2.
<PDBx:pdbx_entity_assemblyCategory>
<PDBx:pdbx_entity_assembly entity_id="1" id="1">
<PDBx:biol_id>1</PDBx:biol_id>
<PDBx:num_copies>1</PDBx:num_copies>
</PDBx:pdbx_entity_assembly>
<PDBx:pdbx_entity_assembly entity_id="2" id="1">
<PDBx:biol_id>1</PDBx:biol_id>
<PDBx:num_copies>1</PDBx:num_copies>
</PDBx:pdbx_entity_assembly>
</PDBx:pdbx_entity_assemblyCategory>
1
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1
1
1
pdbx_entity_assemblyCategory
This property indicates that datablock
has a category element pdbx_entity_assembly.
pdbx_entity_assemblyItem
Abstract Datatype property for pdbx_entity_assembly items.
reference_to_pdbx_entity_assembly
cross-reference to pdbx_entity_assembly
pdbx_entity_assembly.biol_id
An identifier for the assembly.
pdbx_entity_assembly.num_copies
The number of copies of this entity in the assembly.
pdbx_entity_assembly.entity_id
An enity identifier. A reference to attribute id in category entity.
pdbx_entity_assembly.id
An identifier for the assembly.
pdbx_entity_name
The PDBX_ENTITY_NAME records additional name information for
each entity.
Example 1 -
<PDBx:pdbx_entity_nameCategory>
<PDBx:pdbx_entity_name entity_id="1" name="PLASTOCYANIN" name_type="SWS-NAME"></PDBx:pdbx_entity_name>
<PDBx:pdbx_entity_name entity_id="1" name="Electron transport" name_type="SWS-KEYWORD"></PDBx:pdbx_entity_name>
</PDBx:pdbx_entity_nameCategory>
1
1
1
pdbx_entity_nameCategory
This property indicates that datablock
has a category element pdbx_entity_name.
pdbx_entity_nameItem
Abstract Datatype property for pdbx_entity_name items.
reference_to_pdbx_entity_name
cross-reference to pdbx_entity_name
pdbx_entity_name.entity_id
Pointer to attribute id in category entity.
pdbx_entity_name.name
Entity name.
RCSB_NAME
RCSB_SYNONYM
SWS-NAME
SWS-SYNONYM
SWS-KEYWORD
GB-NAME
GB-SYNONYM
GB-KEYWORD
Entity name type.
pdbx_entity_nonpoly
Example 1 -
0
1
0
1
1
pdbx_entity_nonpolyCategory
This property indicates that datablock
has a category element pdbx_entity_nonpoly.
pdbx_entity_nonpolyItem
Abstract Datatype property for pdbx_entity_nonpoly items.
reference_to_pdbx_entity_nonpoly
cross-reference to pdbx_entity_nonpoly
pdbx_entity_nonpoly.comp_id
This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category.
pdbx_entity_nonpoly.name
A name for the non-polymer entity
pdbx_entity_nonpoly.entity_id
This data item is a pointer to attribute id in category entity in the ENTITY category.
pdbx_entity_prod_protocol
This category contains descriptive protocols for the production
of this entity.
1
1
1
1
1
pdbx_entity_prod_protocolCategory
This property indicates that datablock
has a category element pdbx_entity_prod_protocol.
pdbx_entity_prod_protocolItem
Abstract Datatype property for pdbx_entity_prod_protocol items.
reference_to_pdbx_entity_prod_protocol
cross-reference to pdbx_entity_prod_protocol
pdbx_entity_prod_protocol.protocol
The protocol description associated with the protocol_type employed
in the production of this entity.
pdbx_entity_prod_protocol.entity_id
The value of attribute entity_id in category pdbx_entity_prod_protocol uniquely identifies
each protein contained in the project target protein complex whose
structure is to be determined. This data item is a pointer to attribute id
in category entity in the ENTITY category.
pdbx_entity_prod_protocol.entry_id
The value of attribute entry_id in category pdbx_entity_prod_protocol uniquely identifies
a sample consisting of one or more proteins whose structure is
to be determined. This is a pointer to attribute id in category entry.
selection
PCR
cloning
expression
growth
purification
NMR
other
The one of a set of protocol types associated with the production
of this entity.
pdbx_entity_src_gen_character
This category contains details of protein characterisation. It
refers to the characteristion of the product of a specific
step.
0
1
0
1
1
1
1
1
0
1
1
1
1
pdbx_entity_src_gen_characterCategory
This property indicates that datablock
has a category element pdbx_entity_src_gen_character.
pdbx_entity_src_gen_characterItem
Abstract Datatype property for pdbx_entity_src_gen_character items.
reference_to_pdbx_entity_src_gen_character
cross-reference to pdbx_entity_src_gen_character
pdbx_entity_src_gen_character.date
The date of characterisation step.
2003-12-25
2003-12-25:09:00
pdbx_entity_src_gen_character.details
Any details associated with this method of protein characterisation.
pdbx_entity_src_gen_character.method
The method used for protein characterisation.
Dynamic light scattering
Mass spectrometry
pdbx_entity_src_gen_character.result
The result from this method of protein characterisation.
pdbx_entity_src_gen_character.robot_id
This data item is a pointer to pdbx_robot_system.id
in the PDBX_ROBOT_SYSTEM category.
pdbx_entity_src_gen_character.entity_id
The value of attribute entity_id in category pdbx_entity_src_gen_character uniquely identifies
each protein contained in the project target complex proteins whose
structure is to be determined. This data item is a pointer to attribute id
in category entity in the ENTITY category. This item may be a site dependent bar code.
pdbx_entity_src_gen_character.entry_id
The value of attribute entry_id in category pdbx_entity_src_gen_character uniquely identifies
a sample consisting of one or more proteins whose structure is
to be determined. This is a pointer to attribute id in category entry. This item may
be a site dependent bar code.
pdbx_entity_src_gen_character.step_id
This item is the unique identifier for the step whose product
has been characterised.
pdbx_entity_src_gen_chrom
This category contains details for the chromatographic steps used in the
purification of the protein.
1
1
1
1
1
1
0
1
1
1
0
1
0
1
1
1
0
1
1
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
1
1
1
1
1
1
1
pdbx_entity_src_gen_chromCategory
This property indicates that datablock
has a category element pdbx_entity_src_gen_chrom.
pdbx_entity_src_gen_chromItem
Abstract Datatype property for pdbx_entity_src_gen_chrom items.
reference_to_pdbx_entity_src_gen_chrom
cross-reference to pdbx_entity_src_gen_chrom
pdbx_entity_src_gen_chrom.column_temperature
The temperature in degrees celsius at which this column was run.
pdbx_entity_src_gen_chrom.column_type
The type of column used in this step.
pdbx_entity_src_gen_chrom.column_volume
The volume of the column used in this step.
pdbx_entity_src_gen_chrom.date
The date of production step.
2003-12-25
2003-12-25:09:00
pdbx_entity_src_gen_chrom.elution_buffer_id
This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category.
The referenced buffer is that with which the protein was eluted.
pdbx_entity_src_gen_chrom.elution_protocol
Details of the elution protocol.
pdbx_entity_src_gen_chrom.end_construct_id
This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT
category. The referenced sequence is expected to be the amino
acid sequence of the expressed product after the
chromatography step.
pdbx_entity_src_gen_chrom.equilibration_buffer_id
This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category.
The referenced buffer is that in which the column was equilibrated.
pdbx_entity_src_gen_chrom.flow_rate
The rate at which the equilibration buffer flowed through the column.
pdbx_entity_src_gen_chrom.next_step_id
This item unique identifier for the next production step. This allows
a workflow to have multiple entry points leading to a single product.
pdbx_entity_src_gen_chrom.post_treatment
Details of any post-chromatographic treatment of the protein sample.
pdbx_entity_src_gen_chrom.robot_id
This data item is a pointer to pdbx_robot_system.id
in the PDBX_ROBOT_SYSTEM category.
pdbx_entity_src_gen_chrom.sample_conc_method
The method used to determine the concentration of the protein solution put
onto the column.
pdbx_entity_src_gen_chrom.sample_concentration
The concentration of the protein solution put onto the column.
pdbx_entity_src_gen_chrom.sample_prep_details
Details of the sample preparation prior to running the column.
pdbx_entity_src_gen_chrom.sample_volume
The volume of protein solution run on the column.
pdbx_entity_src_gen_chrom.volume_pooled_fractions
The total volume of all the fractions pooled to give the purified protein
solution.
pdbx_entity_src_gen_chrom.yield_method
The method used to determine the yield
pdbx_entity_src_gen_chrom.yield_pooled_fractions
The yield in milligrams of protein recovered in the pooled fractions.
pdbx_entity_src_gen_chrom.entity_id
The value of attribute entity_id in category pdbx_entity_src_gen_chrom uniquely identifies
each protein contained in the project target complex proteins whose
structure is to be determined. This data item is a pointer to attribute id
in category entity in the ENTITY category. This item may be a site dependent bar code.
pdbx_entity_src_gen_chrom.entry_id
The value of attribute entry_id in category pdbx_entity_src_gen_chrom uniquely identifies
a sample consisting of one or more proteins whose structure is
to be determined. This is a pointer to attribute id in category entry. This item may
be a site dependent bar code.
pdbx_entity_src_gen_chrom.step_id
This item is the unique identifier for this chromatography step.
pdbx_entity_src_gen_clone
This category contains details for the cloning steps used in
the overall protein production process. Each row in PDBX_ENTITY_SRC_GEN_CLONE
should have an equivalent row in either PDBX_ENTITY_SRC_GEN_CLONE_LIGATION or
PDBX_ENTITY_SRC_GEN_CLONE_RECOMBINATION. If only summary information is
provided data in the later two categories may be omitted.
0
1
0
1
1
1
0
1
1
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
pdbx_entity_src_gen_cloneCategory
This property indicates that datablock
has a category element pdbx_entity_src_gen_clone.
pdbx_entity_src_gen_cloneItem
Abstract Datatype property for pdbx_entity_src_gen_clone items.
reference_to_pdbx_entity_src_gen_clone
cross-reference to pdbx_entity_src_gen_clone
pdbx_entity_src_gen_clone.date
The date of this production step.
2003-12-25
2003-12-25:09:00
pdbx_entity_src_gen_clone.end_construct_id
This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT
category. The referenced nucleic acid sequence is that of the
cloned product.
L
R
The method used to insert the gene into the vector. For 'Ligation', an
PDBX_ENTITY_SRC_GEN_CLONE_LIGATION entry with matching .step_id is expected. For
'Recombination', an PDBX_ENTITY_SRC_GEN_CLONE_RECOMBINATION entry with matching
.step_id is expected.
A
F
The type of marker included to allow selection of transformed cells
pdbx_entity_src_gen_clone.next_step_id
This item unique identifier for the next production step.
This allows a workflow to have multiple entry points leading
to a single product.
pdbx_entity_src_gen_clone.purification_details
Details of any purification of the product.
pdbx_entity_src_gen_clone.robot_id
This data item is a pointer to pdbx_robot_system.id in the
PDBX_ROBOT_SYSTEM category.
pdbx_entity_src_gen_clone.summary
Summary of ligation or recombionation cloning used, the associated
verification method and any purification of the product.
H
E
C
The method used to transform the expression cell line with the vector
pdbx_entity_src_gen_clone.vector_details
Details of any modifications made to the named vector.
pdbx_entity_src_gen_clone.vector_name
The name of the vector used in this cloning step.
P
R
D
The method used to verify that the incorporated gene is correct
pdbx_entity_src_gen_clone.entity_id
The value of attribute entity_id in category pdbx_entity_src_gen_clone uniquely identifies
each protein contained in the project target protein complex whose
structure is to be determined. This data item is a pointer to attribute id
in category entity in the ENTITY category. This item may be a site dependent bar code.
pdbx_entity_src_gen_clone.entry_id
The value of attribute entry_id in category pdbx_entity_src_gen_clone uniquely identifies
a sample consisting of one or more proteins whose structure is
to be determined. This is a pointer to attribute id in category entry. This item may
be a site dependent bar code.
pdbx_entity_src_gen_clone.step_id
This item is the unique identifier for this cloning step.
pdbx_entity_src_gen_clone_ligation
This category contains details for the ligation-based cloning steps used in
the overall protein production process.
attribute clone_step_id in category pdbx_entity_src_gen_clone_ligation in this category
must point at a defined attribute step_id in category pdbx_entity_src_gen_clone. The details in
PDBX_ENTITY_SRC_GEN_CLONE_LIGATION extend the details in PDBX_ENTITY_SRC_GEN_CLONE
to cover ligation dependent cloning steps.
1
1
0
1
1
1
1
1
1
1
1
1
1
pdbx_entity_src_gen_clone_ligationCategory
This property indicates that datablock
has a category element pdbx_entity_src_gen_clone_ligation.
pdbx_entity_src_gen_clone_ligationItem
Abstract Datatype property for pdbx_entity_src_gen_clone_ligation items.
reference_to_pdbx_entity_src_gen_clone_ligation
cross-reference to pdbx_entity_src_gen_clone_ligation
pdbx_entity_src_gen_clone_ligation.cleavage_enzymes
The names of the enzymes used to cleave the vector. In addition an enzyme
used to blunt the cut ends, etc., should be named here.
pdbx_entity_src_gen_clone_ligation.details
Any details to be associated with this ligation step, e.g. the protocol.
pdbx_entity_src_gen_clone_ligation.ligation_enzymes
The names of the enzymes used to ligate the gene into the cleaved vector.
pdbx_entity_src_gen_clone_ligation.temperature
The temperature at which the ligation experiment was performed, in degrees
celsius.
pdbx_entity_src_gen_clone_ligation.time
The duration of the ligation reaction in minutes.
pdbx_entity_src_gen_clone_ligation.entity_id
This item is a pointer to attribute entity_id in category pdbx_entity_src_gen_clone in the
PDBX_ENTITY_SRC_GEN_CLONE category.
pdbx_entity_src_gen_clone_ligation.entry_id
This item is a pointer to attribute entry_id in category pdbx_entity_src_gen_clone in the
PDBX_ENTITY_SRC_GEN_CLONE category.
pdbx_entity_src_gen_clone_ligation.step_id
This item is a pointer to attribute step_id in category pdbx_entity_src_gen_clone in the
PDBX_ENTITY_SRC_GEN_CLONE category.
pdbx_entity_src_gen_clone_recombination
This category contains details for the recombination-based cloning steps
used in the overall protein production process. It is assumed that these
reactions will use commercially available kits.
attribute clone_step_id in category pdbx_entity_src_gen_clone_recombination in this category
must point at a defined attribute step_id in category pdbx_entity_src_gen_clone. The details in
PDBX_ENTITY_SRC_GEN_CLONE_RECOMBINATION extend the details in PDBX_ENTITY_SRC_GEN_CLONE
to cover recombination dependent cloning steps.
0
1
1
1
1
1
1
1
1
pdbx_entity_src_gen_clone_recombinationCategory
This property indicates that datablock
has a category element pdbx_entity_src_gen_clone_recombination.
pdbx_entity_src_gen_clone_recombinationItem
Abstract Datatype property for pdbx_entity_src_gen_clone_recombination items.
reference_to_pdbx_entity_src_gen_clone_recombination
cross-reference to pdbx_entity_src_gen_clone_recombination
pdbx_entity_src_gen_clone_recombination.details
Any details to be associated with this recombination step, e.g. the protocol
or differences from the manufacturer's specified protocol.
B
L
T
C
I
The names of the enzymes used for this recombination step.
G
I
N
The name of the recombination system.
pdbx_entity_src_gen_clone_recombination.entity_id
This item is a pointer to attribute entity_id in category pdbx_entity_src_gen_clone in the
PDBX_ENTITY_SRC_GEN_CLONE category.
pdbx_entity_src_gen_clone_recombination.entry_id
This item is a pointer to attribute entry_id in category pdbx_entity_src_gen_clone in the
PDBX_ENTITY_SRC_GEN_CLONE category.
pdbx_entity_src_gen_clone_recombination.step_id
This item is a pointer to attribute step_id in category pdbx_entity_src_gen_clone in the
PDBX_ENTITY_SRC_GEN_CLONE category.
pdbx_entity_src_gen_express
This category contains details for the EXPRESSION steps used in
the overall protein production process. It is hoped that this category
will cover all forms of cell-based expression by reading induction as
induction/transformation/transfection.
1
1
1
1
0
1
0
1
1
1
1
1
1
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
0
1
0
1
1
1
1
1
1
1
0
1
0
1
0
1
1
1
1
1
1
pdbx_entity_src_gen_expressCategory
This property indicates that datablock
has a category element pdbx_entity_src_gen_express.
pdbx_entity_src_gen_expressItem
Abstract Datatype property for pdbx_entity_src_gen_express items.
reference_to_pdbx_entity_src_gen_express
cross-reference to pdbx_entity_src_gen_express
pdbx_entity_src_gen_express.C_terminal_seq_tag
Any C-terminal sequence tag as a string of one letter amino acid codes
pdbx_entity_src_gen_express.N_terminal_seq_tag
Any N-terminal sequence tag as a string of one letter amino acid codes.
pdbx_entity_src_gen_express.culture_additives
Any additives to the base media in which the expression host was grown.
pdbx_entity_src_gen_express.culture_base_media
The name of the base media in which the expression host was grown.
pdbx_entity_src_gen_express.culture_temperature
The temperature in degrees celsius at which the expression host was allowed
to grow prior to induction/transformation/transfection.
pdbx_entity_src_gen_express.culture_time
The time in hours for which the expression host was allowed to grow
prior to induction/transformation/transfection.
pdbx_entity_src_gen_express.culture_volume
The volume of media in milliliters in which the expression host was grown.
pdbx_entity_src_gen_express.date
The date of production step.
2003-12-25
2003-12-25:09:00
pdbx_entity_src_gen_express.end_construct_id
This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT
category. The referenced sequence is expected to be the amino
acid sequence of the expressed product.
pdbx_entity_src_gen_express.harvesting_details
Details of the harvesting protocol.
pdbx_entity_src_gen_express.host_org_cell_line
A specific line of cells used as the expression system
pdbx_entity_src_gen_express.host_org_common_name
The common name of the organism that served as host for the
expression system. Where attribute host_org_tax_id
in category pdbx_entity_src_gen_express is populated it is expected that this item may be derived by
look up against the taxonomy database.
pdbx_entity_src_gen_express.host_org_culture_collection
Culture collection of the expression system
pdbx_entity_src_gen_express.host_org_details
A description of special aspects of the organism that served as
host for the expression system.
pdbx_entity_src_gen_express.host_org_scientific_name
The scientific name of the organism that served as host for the
expression system. It is expected that either this item or
attribute host_org_tax_id in category pdbx_entity_src_gen_express should be populated.
pdbx_entity_src_gen_express.host_org_strain
The strain of the organism that served as host for the expression
system. Where attribute host_org_tax_id in category pdbx_entity_src_gen_express is
populated it is expected that this item may be derived by a
look up against the taxonomy database.
pdbx_entity_src_gen_express.host_org_tax_id
The id for the NCBI taxonomy node corresponding to the organism that
served as host for the expression system.
pdbx_entity_src_gen_express.host_org_tissue
The specific tissue which expressed the molecule.
pdbx_entity_src_gen_express.host_org_variant
The vairant of the organism that served as host for the expression
system. Where attribute host_org_tax_id in category pdbx_entity_src_gen_express is
populated it is expected that this item may be derived by a
look up against the taxonomy database.
pdbx_entity_src_gen_express.inducer
The chemical name of the inducing agent.
pdbx_entity_src_gen_express.inducer_concentration
Concentration of the inducing agent.
pdbx_entity_src_gen_express.induction_details
Details of induction/transformation/transfection.
pdbx_entity_src_gen_express.induction_temperature
The temperature in celsius at which the induced/transformed/transfected
cells were grown.
pdbx_entity_src_gen_express.induction_timepoint
The time in hours after induction/transformation/transfection at which
the optical density of the culture was measured.
pdbx_entity_src_gen_express.multiplicity_of_infection
The multiplicity of infection for genes introduced by transfection, eg.
for baculovirus-based expression.
pdbx_entity_src_gen_express.next_step_id
This item unique identifier for the next production step. This allows
a workflow to have multiple entry points leading to a single product.
pdbx_entity_src_gen_express.plasmid_id
This item is a pointer to attribute id in category pdbx_construct in the
PDBX_CONSTRUCT category. The referenced entry will contain
the nucleotide sequence that is to be expressed, including tags.
pdbx_entity_src_gen_express.promoter_type
The nature of the promoter controlling expression of the gene.
T7 LacZ
pdbx_entity_src_gen_express.robot_id
This data item is a pointer to pdbx_robot_system.id
in the PDBX_ROBOT_SYSTEM category.
pdbx_entity_src_gen_express.storage_details
Details of how the harvested culture was stored.
pdbx_entity_src_gen_express.summary
Summary of the details of the expression steps used in protein production.
pdbx_entity_src_gen_express.vector_type
Identifies the type of vector used (plasmid, virus, or cosmid)
in the expression system.
pdbx_entity_src_gen_express.entity_id
The value of attribute entity_id in category pdbx_entity_src_gen_express uniquely identifies
each protein contained in the project target complex proteins whose
structure is to be determined. This data item is a pointer to attribute id
in category entity in the ENTITY category.
This item may be a site dependent bar code.
pdbx_entity_src_gen_express.entry_id
The value of attribute entry_id in category pdbx_entity_src_gen_express uniquely identifies
a sample consisting of one or more proteins whose structure is
to be determined. This is a pointer to attribute id in category entry. This item may
be a site dependent bar code.
pdbx_entity_src_gen_express.step_id
This item is the unique identifier for this expression step.
pdbx_entity_src_gen_express_timepoint
This category contains details for OD time series used to monitor a
given EXPRESSION step used in the overall protein production process.
1
1
1
1
1
1
1
1
pdbx_entity_src_gen_express_timepointCategory
This property indicates that datablock
has a category element pdbx_entity_src_gen_express_timepoint.
pdbx_entity_src_gen_express_timepointItem
Abstract Datatype property for pdbx_entity_src_gen_express_timepoint items.
reference_to_pdbx_entity_src_gen_express_timepoint
cross-reference to pdbx_entity_src_gen_express_timepoint
pdbx_entity_src_gen_express_timepoint.OD
The optical density of the expression culture in arbitrary units at the
timepoint specified.
pdbx_entity_src_gen_express_timepoint.time
The time in hours after induction/transformation/transfection at which
the optical density of the culture was measured.
pdbx_entity_src_gen_express_timepoint.entity_id
The value of attribute entity_id in category pdbx_entity_src_gen_express_timepoint is a pointer
to attribute entity_id in category pdbx_entity_src_gen_express
pdbx_entity_src_gen_express_timepoint.entry_id
The value of attribute entry_id in category pdbx_entity_src_gen_express_timepoint is a pointer
to attribute entry_id in category pdbx_entity_src_gen_express
pdbx_entity_src_gen_express_timepoint.serial
This items uniquely defines a timepoint within a series.
pdbx_entity_src_gen_express_timepoint.step_id
This item is a pointer to attribute step_id in category pdbx_entity_src_gen_express
pdbx_entity_src_gen_fract
This category contains details for the fraction steps used in
the overall protein production process. Examples of fractionation
steps are centrifugation and magnetic bead pull-down purification.
0
1
0
1
0
1
1
1
1
1
1
1
0
1
1
1
1
1
0
1
1
1
1
1
1
pdbx_entity_src_gen_fractCategory
This property indicates that datablock
has a category element pdbx_entity_src_gen_fract.
pdbx_entity_src_gen_fractItem
Abstract Datatype property for pdbx_entity_src_gen_fract items.
reference_to_pdbx_entity_src_gen_fract
cross-reference to pdbx_entity_src_gen_fract
pdbx_entity_src_gen_fract.date
The date of this production step.
2003-12-25
2003-12-25:09:00
pdbx_entity_src_gen_fract.details
String value containing details of the fractionation.
pdbx_entity_src_gen_fract.end_construct_id
This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT
category. The referenced sequence is expected to be the amino
acid sequence of the expressed product after the fractionation
step.
C
M
P
This item describes the method of fractionation.
pdbx_entity_src_gen_fract.next_step_id
This item unique identifier for the next production step. This allows
a workflow to have multiple entry points leading to a single product.
S
P
B
M
A
L
The fraction containing the protein of interest.
pdbx_entity_src_gen_fract.protein_volume
The volume of the fraction containing the protein.
pdbx_entity_src_gen_fract.protein_yield
The yield in milligrams of protein from the fractionation.
pdbx_entity_src_gen_fract.protein_yield_method
The method used to determine the yield
pdbx_entity_src_gen_fract.robot_id
This data item is a pointer to pdbx_robot_system.id
in the PDBX_ROBOT_SYSTEM category.
pdbx_entity_src_gen_fract.temperature
The temperature in degrees celsius at which the fractionation was performed.
pdbx_entity_src_gen_fract.entity_id
The value of attribute entity_id in category pdbx_entity_src_gen_fract uniquely identifies
each protein contained in the project target protein complex whose
structure is to be determined. This data item is a pointer to attribute id
in category entity in the ENTITY category. This item may be a site dependent bar code.
pdbx_entity_src_gen_fract.entry_id
The value of attribute entry_id in category pdbx_entity_src_gen_fract uniquely identifies
a sample consisting of one or more proteins whose structure is
to be determined. This is a pointer to attribute id in category entry. This item may
be a site dependent bar code.
pdbx_entity_src_gen_fract.step_id
This item is the unique identifier for this fractionation step.
pdbx_entity_src_gen_lysis
This category contains details for the cell lysis steps used in
the overall protein production process.
1
1
1
1
0
1
0
1
0
1
1
1
1
1
0
1
1
1
1
1
1
1
1
pdbx_entity_src_gen_lysisCategory
This property indicates that datablock
has a category element pdbx_entity_src_gen_lysis.
pdbx_entity_src_gen_lysisItem
Abstract Datatype property for pdbx_entity_src_gen_lysis items.
reference_to_pdbx_entity_src_gen_lysis
cross-reference to pdbx_entity_src_gen_lysis
pdbx_entity_src_gen_lysis.buffer_id
This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category.
The referenced buffer is that in which the lysis was performed.
pdbx_entity_src_gen_lysis.buffer_volume
The volume in milliliters of buffer in which the lysis was performed.
pdbx_entity_src_gen_lysis.date
The date of this production step.
2003-12-25
2003-12-25:09:00
pdbx_entity_src_gen_lysis.details
String value containing details of the lysis protocol.
pdbx_entity_src_gen_lysis.end_construct_id
This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT
category. The referenced sequence is expected to be the amino
acid sequence of the expressed product after lysis.
S
D
B
The lysis method.
pdbx_entity_src_gen_lysis.next_step_id
This item unique identifier for the next production step. This allows
a workflow to have multiple entry points leading to a single product.
pdbx_entity_src_gen_lysis.robot_id
This data item is a pointer to pdbx_robot_system.id
in the PDBX_ROBOT_SYSTEM category.
pdbx_entity_src_gen_lysis.temperature
The temperature in degrees celsius at which the lysis was performed.
pdbx_entity_src_gen_lysis.time
The time in seconds of the lysis experiment.
pdbx_entity_src_gen_lysis.entity_id
The value of attribute entity_id in category pdbx_entity_src_gen_lysis uniquely identifies
each protein contained in the project target protein complex whose
structure is to be determined. This data item is a pointer to attribute id
in category entity in the ENTITY category. This item may be a site dependent bar code.
pdbx_entity_src_gen_lysis.entry_id
The value of attribute entry_id in category pdbx_entity_src_gen_lysis uniquely identifies
a sample consisting of one or more proteins whose structure is
to be determined. This is a pointer to attribute id in category entry. This item may
be a site dependent bar code.
pdbx_entity_src_gen_lysis.step_id
This item is the unique identifier for this lysis step.
pdbx_entity_src_gen_prod_digest
This category contains details for the DIGEST steps used in
the overall protein production process. The digestion is assumed
to be applied to the result of the previous production step, or the
gene source if this is the first production step.
Example 1 - hypothetical example
<PDBx:pdbx_entity_src_gen_prod_digestCategory>
<PDBx:pdbx_entity_src_gen_prod_digest entity_id="222000111" entry_id="111000111" step_id="2">
<PDBx:date>2002-07-12:15:13</PDBx:date>
<PDBx:end_construct_id>440050000123</PDBx:end_construct_id>
<PDBx:next_step_id>3</PDBx:next_step_id>
<PDBx:purification_details> No purification</PDBx:purification_details>
<PDBx:restriction_enzyme_1>NcoI</PDBx:restriction_enzyme_1>
<PDBx:restriction_enzyme_2>BamII</PDBx:restriction_enzyme_2>
<PDBx:robot_id>5</PDBx:robot_id>
</PDBx:pdbx_entity_src_gen_prod_digest>
</PDBx:pdbx_entity_src_gen_prod_digestCategory>
0
1
0
1
1
1
0
1
1
1
0
1
0
1
0
1
1
1
1
pdbx_entity_src_gen_prod_digestCategory
This property indicates that datablock
has a category element pdbx_entity_src_gen_prod_digest.
pdbx_entity_src_gen_prod_digestItem
Abstract Datatype property for pdbx_entity_src_gen_prod_digest items.
reference_to_pdbx_entity_src_gen_prod_digest
cross-reference to pdbx_entity_src_gen_prod_digest
pdbx_entity_src_gen_prod_digest.date
The date of this production step.
2003-12-25
pdbx_entity_src_gen_prod_digest.end_construct_id
This item is a pointer to pdbx_construct.id in the
PDBX_CONSTRUCT category. The referenced nucleic acid sequence
is that of the digest product
pdbx_entity_src_gen_prod_digest.next_step_id
This item unique identifier for the next production step. This allows
a workflow to have multiple entry points leading to a single product.
pdbx_entity_src_gen_prod_digest.purification_details
String value containing details of any purification of the
product of the digestion.
pdbx_entity_src_gen_prod_digest.restriction_enzyme_1
The first enzyme used in the restriction digestion. The sites at
which this cuts can be derived from the sequence.
BamIII
pdbx_entity_src_gen_prod_digest.restriction_enzyme_2
The second enzyme used in the restriction digestion. The sites at
which this cuts can be derived from the sequence.
pdbx_entity_src_gen_prod_digest.robot_id
This data item is a pointer to pdbx_robot_system.id
in the PDBX_ROBOT_SYSTEM category.
pdbx_entity_src_gen_prod_digest.summary
Summary of the details of restriction digestion any purification of the
product of the digestion.
pdbx_entity_src_gen_prod_digest.entity_id
The value of attribute entity_id in category pdbx_entity_src_gen_prod_digest uniquely identifies
each protein contained in the project target protein complex whose
structure is to be determined. This data item is a pointer to attribute id
in category entity in the ENTITY category. This item may be a site dependent bar code.
pdbx_entity_src_gen_prod_digest.entry_id
The value of attribute entry_id in category pdbx_entity_src_gen_prod_digest uniquely identifies
a sample consisting of one or more proteins whose structure is
to be determined. This is a pointer to attribute id in category entry. This item may
be a site dependent bar code.
pdbx_entity_src_gen_prod_digest.step_id
This item is the unique identifier for this digestion step.
pdbx_entity_src_gen_prod_other
This category contains details for process steps that are
not explicitly catered for elsewhere. It provides some basic
details as well as placeholders for a list of parameters and
values (the category PDBX_ENTITY_SRC_GEN_PROD_OTHER_PARAMETER).
Note that processes that have been modelled explicitly should
not be represented using this category.
0
1
0
1
0
1
1
1
0
1
0
1
1
1
1
pdbx_entity_src_gen_prod_otherCategory
This property indicates that datablock
has a category element pdbx_entity_src_gen_prod_other.
pdbx_entity_src_gen_prod_otherItem
Abstract Datatype property for pdbx_entity_src_gen_prod_other items.
reference_to_pdbx_entity_src_gen_prod_other
cross-reference to pdbx_entity_src_gen_prod_other
pdbx_entity_src_gen_prod_other.date
The date of this process step.
2003-12-25
2003-12-25:09:00
pdbx_entity_src_gen_prod_other.details
Additional details of this process step.
pdbx_entity_src_gen_prod_other.end_construct_id
This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT
category. The referenced nucleic acid sequence is that of the
product of the process step.
pdbx_entity_src_gen_prod_other.next_step_id
This item unique identifier for the next production step.
This allows a workflow to have multiple entry points leading
to a single product.
pdbx_entity_src_gen_prod_other.process_name
Name of this process step.
pdbx_entity_src_gen_prod_other.robot_id
This data item is a pointer to pdbx_robot_system.id in the
PDBX_ROBOT_SYSTEM category. The referenced robot is the
robot responsible for the process step
pdbx_entity_src_gen_prod_other.entity_id
The value of attribute entity_id in category pdbx_entity_src_gen_prod_other uniquely identifies
each protein contained in the project target protein complex whose
structure is to be determined. This data item is a pointer to attribute id
in category entity in the ENTITY category. This item may be a site dependent bar code.
pdbx_entity_src_gen_prod_other.entry_id
The value of attribute entry_id in category pdbx_entity_src_gen_prod_other uniquely identifies
a sample consisting of one or more proteins whose structure is
to be determined. This is a pointer to attribute id in category entry. This item may
be a site dependent bar code.
pdbx_entity_src_gen_prod_other.step_id
This item is the unique identifier for this process step.
pdbx_entity_src_gen_prod_other_parameter
This category contains parameters and values required to capture
information about a particular process step
1
1
1
1
1
1
1
1
pdbx_entity_src_gen_prod_other_parameterCategory
This property indicates that datablock
has a category element pdbx_entity_src_gen_prod_other_parameter.
pdbx_entity_src_gen_prod_other_parameterItem
Abstract Datatype property for pdbx_entity_src_gen_prod_other_parameter items.
reference_to_pdbx_entity_src_gen_prod_other_parameter
cross-reference to pdbx_entity_src_gen_prod_other_parameter
pdbx_entity_src_gen_prod_other_parameter.details
Additional details about the parameter
pdbx_entity_src_gen_prod_other_parameter.value
The value of the parameter
pdbx_entity_src_gen_prod_other_parameter.entity_id
The value of attribute entity_id in category pdbx_entity_src_gen_prod_other_parameter is a pointer
to attribute entity_id in category pdbx_entity_src_gen_prod_other
pdbx_entity_src_gen_prod_other_parameter.entry_id
The value of attribute entry_id in category pdbx_entity_src_gen_prod_other_parameter is a pointer
to attribute entry.id in category pdbx_entity_src_gen_prod_other
pdbx_entity_src_gen_prod_other_parameter.parameter
The name of the parameter associated with the process step
pdbx_entity_src_gen_prod_other_parameter.step_id
This item is a pointer to attribute step_id in category pdbx_entity_src_gen_prod_other
pdbx_entity_src_gen_prod_pcr
This category contains details for the PCR steps used in
the overall protein production process. The PCR is assumed
to be applied to the result of the previous production step, or the
gene source if this is the first production step.
Example 1 - hypothetical example
<PDBx:pdbx_entity_src_gen_prod_pcrCategory>
<PDBx:pdbx_entity_src_gen_prod_pcr entity_id="222000111" entry_id="111000111" step_id="1">
<PDBx:date>2002-07-12:15:13</PDBx:date>
<PDBx:end_construct_id>440050000111</PDBx:end_construct_id>
<PDBx:forward_primer_id>2</PDBx:forward_primer_id>
<PDBx:next_step_id>2</PDBx:next_step_id>
<PDBx:purification_details> No purification</PDBx:purification_details>
<PDBx:reaction_details> Annealing temperature = 70 C
Annealing time = 60 s
Extending temperature = 74 C
Extending time = 120 s
Melting temperature = 95 C
Melting time = 120 s
Number of cycles = 40
Polymerase = KOD
Template = 10 pmol
Primer = 25 pmol
Total volume = 25 ul</PDBx:reaction_details>
<PDBx:reverse_primer_id>3</PDBx:reverse_primer_id>
<PDBx:robot_id>5</PDBx:robot_id>
</PDBx:pdbx_entity_src_gen_prod_pcr>
</PDBx:pdbx_entity_src_gen_prod_pcrCategory>
0
1
0
1
1
1
1
1
0
1
0
1
1
1
0
1
0
1
1
1
1
pdbx_entity_src_gen_prod_pcrCategory
This property indicates that datablock
has a category element pdbx_entity_src_gen_prod_pcr.
pdbx_entity_src_gen_prod_pcrItem
Abstract Datatype property for pdbx_entity_src_gen_prod_pcr items.
reference_to_pdbx_entity_src_gen_prod_pcr
cross-reference to pdbx_entity_src_gen_prod_pcr
pdbx_entity_src_gen_prod_pcr.date
The date of this production step.
2003-12-25
2003-12-25:09:00
pdbx_entity_src_gen_prod_pcr.end_construct_id
This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT
category. The referenced nucleic acid sequence is that of the
PCR product.
pdbx_entity_src_gen_prod_pcr.forward_primer_id
This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category.
The referenced nucleic acid sequence is that of the forward primer.
pdbx_entity_src_gen_prod_pcr.next_step_id
This item unique identifier for the next production step.
This allows a workflow to have multiple entry points leading
to a single product.
pdbx_entity_src_gen_prod_pcr.purification_details
String value containing details of any purification of the
product of the PCR reaction.
pdbx_entity_src_gen_prod_pcr.reaction_details
String value containing details of the PCR reaction.
pdbx_entity_src_gen_prod_pcr.reverse_primer_id
This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category.
The referenced nucleic acid sequence is that of the reverse primer.
pdbx_entity_src_gen_prod_pcr.robot_id
This data item is a pointer to pdbx_robot_system.id in the
PDBX_ROBOT_SYSTEM category. The referenced robot is the
robot responsible for the PCR reaction (normally the heat
cycler).
pdbx_entity_src_gen_prod_pcr.summary
Summary of the details of the PCR reaction any purification of the
product of the PCR reaction.
pdbx_entity_src_gen_prod_pcr.entity_id
The value of attribute entity_id in category pdbx_entity_src_gen_prod_pcr uniquely identifies
each protein contained in the project target protein complex whose
structure is to be determined. This data item is a pointer to attribute id
in category entity in the ENTITY category. This item may be a site dependent bar code.
pdbx_entity_src_gen_prod_pcr.entry_id
The value of attribute entry_id in category pdbx_entity_src_gen_prod_pcr uniquely identifies
a sample consisting of one or more proteins whose structure is
to be determined. This is a pointer to attribute id in category entry. This item may
be a site dependent bar code.
pdbx_entity_src_gen_prod_pcr.step_id
This item is the unique identifier for this PCR step.
pdbx_entity_src_gen_proteolysis
This category contains details for the protein purification
tag removal steps used in the overall protein production process
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
0
1
0
1
1
1
1
pdbx_entity_src_gen_proteolysisCategory
This property indicates that datablock
has a category element pdbx_entity_src_gen_proteolysis.
pdbx_entity_src_gen_proteolysisItem
Abstract Datatype property for pdbx_entity_src_gen_proteolysis items.
reference_to_pdbx_entity_src_gen_proteolysis
cross-reference to pdbx_entity_src_gen_proteolysis
pdbx_entity_src_gen_proteolysis.cleavage_buffer_id
This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category.
The referenced buffer is that in which the cleavage was performed.
pdbx_entity_src_gen_proteolysis.cleavage_temperature
The temperature in degrees celsius at which the cleavage was performed.
pdbx_entity_src_gen_proteolysis.cleavage_time
The time in minutes for the cleavage reaction
pdbx_entity_src_gen_proteolysis.date
The date of production step.
2003-12-25
2003-12-25:09:00
pdbx_entity_src_gen_proteolysis.details
Details of this tag removal step.
pdbx_entity_src_gen_proteolysis.end_construct_id
This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT
category. The referenced sequence is expected to be the amino
acid sequence of the expressed product after the proteolysis
step.
pdbx_entity_src_gen_proteolysis.next_step_id
This item unique identifier for the next production step. This allows
a workflow to have multiple entry points leading to a single product.
pdbx_entity_src_gen_proteolysis.protease
The name of the protease used for cleavage.
pdbx_entity_src_gen_proteolysis.protein_protease_ratio
The ratio of protein to protease used for the cleavage.
= mol protein / mol protease
pdbx_entity_src_gen_proteolysis.robot_id
This data item is a pointer to pdbx_robot_system.id
in the PDBX_ROBOT_SYSTEM category.
pdbx_entity_src_gen_proteolysis.entity_id
The value of attribute entity_id in category pdbx_entity_src_gen_proteolysis uniquely identifies
each protein contained in the project target complex proteins whose
structure is to be determined. This data item is a pointer to attribute id
in category entity in the ENTITY category. This item may be a site dependent bar code.
pdbx_entity_src_gen_proteolysis.entry_id
The value of attribute entry_id in category pdbx_entity_src_gen_proteolysis uniquely identifies
a sample consisting of one or more proteins whose structure is
to be determined. This is a pointer to attribute id in category entry. This item may
be a site dependent bar code.
pdbx_entity_src_gen_proteolysis.step_id
This item is the unique identifier for this tag removal step.
pdbx_entity_src_gen_pure
This category contains details for the final purified protein product. Note
that this category does not contain the amino acid sequence of the protein.
The sequence will be found in the ENTITY_POLY_SEQ entry with matching
entity_id.
Only one PDBX_ENTITY_SRC_GEN_PURE category is allowed per entity, hence there is
no step_id for this category.
1
1
0
1
0
1
0
1
0
1
1
1
0
1
0
1
0
1
1
1
0
1
0
1
1
1
1
pdbx_entity_src_gen_pureCategory
This property indicates that datablock
has a category element pdbx_entity_src_gen_pure.
pdbx_entity_src_gen_pureItem
Abstract Datatype property for pdbx_entity_src_gen_pure items.
reference_to_pdbx_entity_src_gen_pure
cross-reference to pdbx_entity_src_gen_pure
pdbx_entity_src_gen_pure.conc_assay_method
The method used to measure the protein concentration
pdbx_entity_src_gen_pure.conc_details
Details of the protein concentration procedure
pdbx_entity_src_gen_pure.conc_device_id
This data item is a pointer to pdbx_robot_system.id
in the PDBX_ROBOT_SYSTEM category.
pdbx_entity_src_gen_pure.date
The date of production step.
2003-12-25
2003-12-25:09:00
pdbx_entity_src_gen_pure.product_id
When present, this item should be a globally unique identifier
that identifies the final product. It is envisaged that this
should be the same as and product code associated with the
sample and would provide the key by which information about
the production process may be extracted from the protein
production facility. For files describing the protein
production process (i.e. where attribute type in category entity is 'P' or 'E')
this should have the same value as attribute id in category entry
pdbx_entity_src_gen_pure.protein_concentration
The final concentration of the protein.
pdbx_entity_src_gen_pure.protein_oligomeric_state
The oligomeric state of the protein. Monomeric is 1, dimeric 2, etc.
pdbx_entity_src_gen_pure.protein_purity
The purity of the protein (percent).
pdbx_entity_src_gen_pure.protein_yield
The yield of protein in milligrams.
pdbx_entity_src_gen_pure.storage_buffer_id
This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category.
The referenced buffer is that in which the protein was stored.
pdbx_entity_src_gen_pure.storage_temperature
The temperature in degrees celsius at which the protein was stored.
pdbx_entity_src_gen_pure.summary
Summary of the details of protein purification method used to obtain the final
protein product. This description should include any lysis, fractionation,
proteolysis, refolding, chromatography used as well as the method used the
characterize the final product.
pdbx_entity_src_gen_pure.entity_id
The value of attribute entity_id in category pdbx_entity_src_gen_pure uniquely identifies
each protein contained in the project target complex proteins whose
structure is to be determined. This data item is a pointer to attribute id
in category entity in the ENTITY category. This item may be a site dependent bar code.
pdbx_entity_src_gen_pure.entry_id
The value of attribute entry_id in category pdbx_entity_src_gen_pure uniquely identifies
a sample consisting of one or more proteins whose structure is
to be determined. This is a pointer to attribute id in category entry. This item may
be a site dependent bar code.
pdbx_entity_src_gen_pure.step_id
This item unique identifier the production step.
pdbx_entity_src_gen_refold
This category contains details for the refolding steps used in
the overall protein production process.
0
1
1
1
0
1
0
1
1
1
1
1
0
1
1
1
1
1
1
1
1
1
1
pdbx_entity_src_gen_refoldCategory
This property indicates that datablock
has a category element pdbx_entity_src_gen_refold.
pdbx_entity_src_gen_refoldItem
Abstract Datatype property for pdbx_entity_src_gen_refold items.
reference_to_pdbx_entity_src_gen_refold
cross-reference to pdbx_entity_src_gen_refold
pdbx_entity_src_gen_refold.date
The date of this production step.
2003-12-25
2003-12-25:09:00
pdbx_entity_src_gen_refold.denature_buffer_id
This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category.
The referenced buffer is that in which the protein was denatured.
pdbx_entity_src_gen_refold.details
String value containing details of the refolding.
pdbx_entity_src_gen_refold.end_construct_id
This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT
category. The referenced sequence is expected to be the amino
acid sequence of the expressed product after the refolding
step.
pdbx_entity_src_gen_refold.next_step_id
This item unique identifier for the next production step. This allows
a workflow to have multiple entry points leading to a single product.
pdbx_entity_src_gen_refold.refold_buffer_id
This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category.
The referenced buffer is that in which the protein was refolded.
pdbx_entity_src_gen_refold.robot_id
This data item is a pointer to pdbx_robot_system.id
in the PDBX_ROBOT_SYSTEM category.
pdbx_entity_src_gen_refold.storage_buffer_id
This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category.
The referenced buffer is that in which the refolded protein was stored.
pdbx_entity_src_gen_refold.temperature
The temperature in degrees celsius at which the protein was refolded.
pdbx_entity_src_gen_refold.time
The time in hours over which the protein was refolded.
pdbx_entity_src_gen_refold.entity_id
The value of attribute entity_id in category pdbx_entity_src_gen_refold uniquely identifies
each protein contained in the project target protein complex whose
structure is to be determined. This data item is a pointer to attribute id
in category entity in the ENTITY category. This item may be a site dependent bar code.
pdbx_entity_src_gen_refold.entry_id
The value of attribute entry_id in category pdbx_entity_src_gen_refold uniquely identifies
a sample consisting of one or more proteins whose structure is
to be determined. This is a pointer to attribute id in category entry. This item may
be a site dependent bar code.
pdbx_entity_src_gen_refold.step_id
This item is the unique identifier for this refolding step.
pdbx_entity_src_syn
PDBX_ENTITY_SRC_SYN records the details about each chemically
synthesized molecule (entity) in the asymmetric unit.
0
1
0
1
0
1
0
1
1
pdbx_entity_src_synCategory
This property indicates that datablock
has a category element pdbx_entity_src_syn.
pdbx_entity_src_synItem
Abstract Datatype property for pdbx_entity_src_syn items.
reference_to_pdbx_entity_src_syn
cross-reference to pdbx_entity_src_syn
pdbx_entity_src_syn.details
A description of special aspects of the source for the
synthetic entity.
This sequence occurs naturally in humans.
pdbx_entity_src_syn.ncbi_taxonomy_id
NCBI Taxonomy identifier of the organism from which the sequence of
the synthetic entity was derived.
Reference:
Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD,
Tatusova TA, Rapp BA (2000). Database resources of the National
Center for Biotechnology Information. Nucleic Acids Res 2000 Jan
1;28(1):10-4
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA,
Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.
pdbx_entity_src_syn.organism_common_name
The common name of the organism from which the sequence of
the synthetic entity was derived.
house mouse
pdbx_entity_src_syn.organism_scientific
The scientific name of the organism from which the sequence of
the synthetic entity was derived.
Mus musculus
pdbx_entity_src_syn.entity_id
This data item is a pointer to attribute id in category entity in the ENTITY category.
1
2
3
4
pdbx_entry_details
Data items in the PDBX_ENTRY_DETAILS category provide additional
details about this entry.
Example 1
<PDBx:pdbx_entry_detailsCategory>
<PDBx:pdbx_entry_details entry_id="1ABC">
<PDBx:nonpolymer_details>Inhibitor VX4A in this entry adopts a highly strained conformation
about C32 inorder to fit into the cleft about the active site.</PDBx:nonpolymer_details>
</PDBx:pdbx_entry_details>
</PDBx:pdbx_entry_detailsCategory>
0
1
0
1
0
1
0
1
1
pdbx_entry_detailsCategory
This property indicates that datablock
has a category element pdbx_entry_details.
pdbx_entry_detailsItem
Abstract Datatype property for pdbx_entry_details items.
reference_to_pdbx_entry_details
cross-reference to pdbx_entry_details
pdbx_entry_details.compound_details
Additional details about the macromolecular compounds in this entry.
pdbx_entry_details.nonpolymer_details
Additional details about the non-polymer components in this entry.
pdbx_entry_details.sequence_details
Additional details about the sequence or sequence database correspondences
for this entry.
pdbx_entry_details.source_details
Additional details about the source and taxonomy of the macromolecular
components in this entry.
pdbx_entry_details.entry_id
This item identifies the entry. This is a reference to attribute id in category entry.
pdbx_exptl_crystal_cryo_treatment
Data items in the PDBX_EXPTL_CRYSTAL_CRYO_TREATMENT category
record details cryogenic treatments applied to this crystal.
Example 1
<PDBx:pdbx_exptl_crystal_cryo_treatmentCategory>
<PDBx:pdbx_exptl_crystal_cryo_treatment crystal_id="4">
<PDBx:annealing_details xsi:nil="true" />
<PDBx:cooling_details> Direct immersion in liquid nitrogen</PDBx:cooling_details>
<PDBx:final_solution_details> 25% (v/v) glycerol in precipitant solution</PDBx:final_solution_details>
<PDBx:soaking_details> A series of 1 min soaks beginning at 5% (v/v) glycerol in precipitant,
transiting to 20% (v/v) glycerol, and finally to 25% glycerol</PDBx:soaking_details>
</PDBx:pdbx_exptl_crystal_cryo_treatment>
</PDBx:pdbx_exptl_crystal_cryo_treatmentCategory>
0
1
0
1
0
1
0
1
1
pdbx_exptl_crystal_cryo_treatmentCategory
This property indicates that datablock
has a category element pdbx_exptl_crystal_cryo_treatment.
pdbx_exptl_crystal_cryo_treatmentItem
Abstract Datatype property for pdbx_exptl_crystal_cryo_treatment items.
reference_to_pdbx_exptl_crystal_cryo_treatment
cross-reference to pdbx_exptl_crystal_cryo_treatment
pdbx_exptl_crystal_cryo_treatment.annealing_details
Details of the annealing treatment applied to this crystal.
10 sec interruption of cold stream with plastic ruler.
Performed twice.
pdbx_exptl_crystal_cryo_treatment.cooling_details
Details of the cooling treatment applied to this crystal.
Direct immersion in liquid nitrogen
pdbx_exptl_crystal_cryo_treatment.final_solution_details
Details of the final solution used in the treatment of this crystal
25% (v/v) glycerol in precipitant solution
pdbx_exptl_crystal_cryo_treatment.soaking_details
Details of the soaking treatment applied to this crystal.
A series of 1 min soaks beginning at 5% (v/v) glycerol in precipitant,
transiting to 20% (v/v) glycerol, and finally to 25% glycerol
pdbx_exptl_crystal_cryo_treatment.crystal_id
This data item is a pointer to attribute id in category exptl_crystal in the
EXPTL_CRYSTAL category.
pdbx_exptl_crystal_grow_comp
Data items in the PDBX_EXPTL_CRYSTAL_GROW_COMP category record
details about the components of the solutions that were 'mixed'
to produce the crystal.
Example 1 -
<PDBx:pdbx_exptl_crystal_grow_compCategory>
<PDBx:pdbx_exptl_crystal_grow_comp comp_id="1" crystal_id="4">
<PDBx:comp_name>protein</PDBx:comp_name>
<PDBx:conc>25.</PDBx:conc>
<PDBx:conc_range></PDBx:conc_range>
<PDBx:conc_units>mg/ml</PDBx:conc_units>
<PDBx:sol_id>protein</PDBx:sol_id>
</PDBx:pdbx_exptl_crystal_grow_comp>
<PDBx:pdbx_exptl_crystal_grow_comp comp_id="2" crystal_id="4">
<PDBx:comp_name>Tris HCl</PDBx:comp_name>
<PDBx:conc>20.</PDBx:conc>
<PDBx:conc_range></PDBx:conc_range>
<PDBx:conc_units>millimolar</PDBx:conc_units>
<PDBx:sol_id>protein</PDBx:sol_id>
</PDBx:pdbx_exptl_crystal_grow_comp>
<PDBx:pdbx_exptl_crystal_grow_comp comp_id="3" crystal_id="4">
<PDBx:comp_name>NaCl</PDBx:comp_name>
<PDBx:conc>0.2</PDBx:conc>
<PDBx:conc_range></PDBx:conc_range>
<PDBx:conc_units>molar</PDBx:conc_units>
<PDBx:sol_id>protein</PDBx:sol_id>
</PDBx:pdbx_exptl_crystal_grow_comp>
<PDBx:pdbx_exptl_crystal_grow_comp comp_id="1" crystal_id="4">
<PDBx:comp_name>PEG 4000</PDBx:comp_name>
<PDBx:conc>12.5</PDBx:conc>
<PDBx:conc_range></PDBx:conc_range>
<PDBx:conc_units>percent_weight_by_volume</PDBx:conc_units>
<PDBx:sol_id>precipitant</PDBx:sol_id>
</PDBx:pdbx_exptl_crystal_grow_comp>
<PDBx:pdbx_exptl_crystal_grow_comp comp_id="2" crystal_id="4">
<PDBx:comp_name>MES</PDBx:comp_name>
<PDBx:conc>0.1</PDBx:conc>
<PDBx:conc_range></PDBx:conc_range>
<PDBx:conc_units>molar</PDBx:conc_units>
<PDBx:sol_id>precipitant</PDBx:sol_id>
</PDBx:pdbx_exptl_crystal_grow_comp>
</PDBx:pdbx_exptl_crystal_grow_compCategory>
0
1
0
1
0
1
0
1
0
1
1
1
pdbx_exptl_crystal_grow_compCategory
This property indicates that datablock
has a category element pdbx_exptl_crystal_grow_comp.
pdbx_exptl_crystal_grow_compItem
Abstract Datatype property for pdbx_exptl_crystal_grow_comp items.
reference_to_pdbx_exptl_crystal_grow_comp
cross-reference to pdbx_exptl_crystal_grow_comp
pdbx_exptl_crystal_grow_comp.comp_name
A common name for the component of the solution.
protein in buffer
acetic acid
pdbx_exptl_crystal_grow_comp.conc
The concentration value of the solution component.
200.
0.1
pdbx_exptl_crystal_grow_comp.conc_range
The concentration range of the solution component.
200. - 230.
0.1 - 0.2
pdbx_exptl_crystal_grow_comp.conc_units
The concentration units for the solution component.
millimolar
percent_weight_by_volume
milligrams_per_milliliter
pdbx_exptl_crystal_grow_comp.sol_id
An identifier for the solution to which the given solution
component belongs.
pdbx_exptl_crystal_grow_comp.comp_id
The value of attribute comp_id in category exptl_crystal_grow_comp must uniquely identify
each item in the PDBX_EXPTL_CRYSTAL_GROW_COMP list.
Note that this item need not be a number; it can be any unique
identifier.
1
2
pdbx_exptl_crystal_grow_comp.crystal_id
This data item is a pointer to attribute id in category exptl_crystal in the
EXPTL_CRYSTAL category.
pdbx_exptl_crystal_grow_sol
Data items in the PDBX_EXPTL_CRYSTAL_GROW_SOL category record
details about the solutions that were 'mixed'
to produce the crystal.
Example 1
<PDBx:pdbx_exptl_crystal_grow_solCategory>
<PDBx:pdbx_exptl_crystal_grow_sol crystal_id="1" sol_id="protein">
<PDBx:pH>7.5</PDBx:pH>
<PDBx:volume>0.5</PDBx:volume>
<PDBx:volume_units>microliter</PDBx:volume_units>
</PDBx:pdbx_exptl_crystal_grow_sol>
<PDBx:pdbx_exptl_crystal_grow_sol crystal_id="1" sol_id="precipitant">
<PDBx:pH>7.3</PDBx:pH>
<PDBx:volume>0.5</PDBx:volume>
<PDBx:volume_units>microliter</PDBx:volume_units>
</PDBx:pdbx_exptl_crystal_grow_sol>
<PDBx:pdbx_exptl_crystal_grow_sol crystal_id="1" sol_id="reservoir">
<PDBx:pH>7.3</PDBx:pH>
<PDBx:volume>0.5</PDBx:volume>
<PDBx:volume_units>milliliter</PDBx:volume_units>
</PDBx:pdbx_exptl_crystal_grow_sol>
</PDBx:pdbx_exptl_crystal_grow_solCategory>
0
1
0
1
0
1
1
1
pdbx_exptl_crystal_grow_solCategory
This property indicates that datablock
has a category element pdbx_exptl_crystal_grow_sol.
pdbx_exptl_crystal_grow_solItem
Abstract Datatype property for pdbx_exptl_crystal_grow_sol items.
reference_to_pdbx_exptl_crystal_grow_sol
cross-reference to pdbx_exptl_crystal_grow_sol
pdbx_exptl_crystal_grow_sol.pH
The pH of the solution.
7.2
pdbx_exptl_crystal_grow_sol.volume
The volume of the solution.
200.
0.1
pdbx_exptl_crystal_grow_sol.volume_units
The volume units of the solution.
milliliter
micoliter
pdbx_exptl_crystal_grow_sol.crystal_id
This data item is a pointer to attribute id in category exptl_crystal in the
EXPTL_CRYSTAL category.
precipitant
reservoir
macromolecule
An identifier for this solution (e.g. precipitant, reservoir, macromolecule)
pdbx_exptl_pd
Data items in the pdbx_exptl_pd record information about
powder sample preparations.
0
1
0
1
0
1
1
pdbx_exptl_pdCategory
This property indicates that datablock
has a category element pdbx_exptl_pd.
pdbx_exptl_pdItem
Abstract Datatype property for pdbx_exptl_pd items.
reference_to_pdbx_exptl_pd
cross-reference to pdbx_exptl_pd
pdbx_exptl_pd.spec_preparation
A description of preparation steps for producing the
diffraction specimen from the sample. Include any procedures
related to grinding, sieving, spray drying, etc.
POLYCRYSTAL SLURRY
wet grinding in acetone
sieved through a 44 micron (325 mesh/inch) sieve
spray dried in water with 1% clay
pdbx_exptl_pd.spec_preparation_pH
The pH at which the powder sample was prepared.
pdbx_exptl_pd.spec_preparation_pH_range
The range of pH values at which the sample was prepared. Used when
a point estimate of pH is not appropriate.
5.6 - 6.4
pdbx_exptl_pd.entry_id
The value of attribute entry_id in category pdbx_exptl_pd uniquely identifies a
record in the PDBX_EXPTL_PD category.
pdbx_feature_assembly
Data items in the PDBX_FEATURE_ASSEMBLY category records
information about properties pertaining to this
structural assembly.
Example 1 - Biological process for functional assembly
<PDBx:pdbx_feature_assemblyCategory>
<PDBx:pdbx_feature_assembly id="1">
<PDBx:assembly_id>b1</PDBx:assembly_id>
<PDBx:feature>nitrogen metabolism</PDBx:feature>
<PDBx:feature_assigned_by>GO</PDBx:feature_assigned_by>
<PDBx:feature_citation_id>GO</PDBx:feature_citation_id>
<PDBx:feature_name>biological process</PDBx:feature_name>
<PDBx:feature_type>value</PDBx:feature_type>
</PDBx:pdbx_feature_assembly>
</PDBx:pdbx_feature_assemblyCategory>
1
1
1
1
1
1
0
1
0
1
1
1
0
1
1
1
1
pdbx_feature_assemblyCategory
This property indicates that datablock
has a category element pdbx_feature_assembly.
pdbx_feature_assemblyItem
Abstract Datatype property for pdbx_feature_assembly items.
reference_to_pdbx_feature_assembly
cross-reference to pdbx_feature_assembly
pdbx_feature_assembly.assembly_id
The value of attribute assembly_id in category pdbx_feature_assembly references an
assembly definition in category STRUCT_BIOL
pdbx_feature_assembly.feature
The value of attribute feature_name in category pdbx_feature_assembly.
pdbx_feature_assembly.feature_assigned_by
attribute feature_assigned_by in category pdbx_feature_assembly identifies
the individual, organization or program that assigned
the feature.
pdbx_feature_assembly.feature_citation_id
attribute feature_citation_id in category pdbx_feature_assembly is a
reference to a citation in the CITATION category
pdbx_feature_assembly.feature_identifier
attribute feature_identifier in category pdbx_feature_assembly_range is an
additional identifier used to identify or
accession this feature.
pdbx_feature_assembly.feature_name
attribute feature_name in category pdbx_feature_assembly identifies a feature
by name.
pdbx_feature_assembly.feature_software_id
attribute feature_software_id in category pdbx_feature_assembly is a
reference to an application described in the
SOFTWARE category.
value
uri
attribute feature_type in category pdbx_feature_assembly identifies the
type of feature.
pdbx_feature_assembly.id
The value of attribute id in category pdbx_feature_assembly uniquely identifies a
feature in the PDBX_FEATURE_ASSEMBLY category.
pdbx_feature_domain
Data items in the PDBX_FEATURE_DOMAIN category records
information about properties pertaining to this structure
domain.
Example 1 - SCOP data for PDB Entry 1KIP domain d1kipa_
<PDBx:pdbx_feature_domainCategory>
<PDBx:pdbx_feature_domain id="1">
<PDBx:domain_id>d1kipa_</PDBx:domain_id>
<PDBx:feature>All beta proteins</PDBx:feature>
<PDBx:feature_assigned_by>SCOP</PDBx:feature_assigned_by>
<PDBx:feature_citation_id>scop</PDBx:feature_citation_id>
<PDBx:feature_name>class</PDBx:feature_name>
<PDBx:feature_type>value</PDBx:feature_type>
</PDBx:pdbx_feature_domain>
<PDBx:pdbx_feature_domain id="2">
<PDBx:domain_id>d1kipa_</PDBx:domain_id>
<PDBx:feature>Immunoglobulin-like beta-sandwich</PDBx:feature>
<PDBx:feature_assigned_by>SCOP</PDBx:feature_assigned_by>
<PDBx:feature_citation_id>scop</PDBx:feature_citation_id>
<PDBx:feature_name>fold</PDBx:feature_name>
<PDBx:feature_type>value</PDBx:feature_type>
</PDBx:pdbx_feature_domain>
<PDBx:pdbx_feature_domain id="3">
<PDBx:domain_id>d1kipa_</PDBx:domain_id>
<PDBx:feature>Immunoglobulin</PDBx:feature>
<PDBx:feature_assigned_by>SCOP</PDBx:feature_assigned_by>
<PDBx:feature_citation_id>scop</PDBx:feature_citation_id>
<PDBx:feature_name>superfamily</PDBx:feature_name>
<PDBx:feature_type>value</PDBx:feature_type>
</PDBx:pdbx_feature_domain>
<PDBx:pdbx_feature_domain id="4">
<PDBx:domain_id>d1kipa_</PDBx:domain_id>
<PDBx:feature>V set domains (antibody variable domain-like)</PDBx:feature>
<PDBx:feature_assigned_by>SCOP</PDBx:feature_assigned_by>
<PDBx:feature_citation_id>scop</PDBx:feature_citation_id>
<PDBx:feature_name>family</PDBx:feature_name>
<PDBx:feature_type>value</PDBx:feature_type>
</PDBx:pdbx_feature_domain>
<PDBx:pdbx_feature_domain id="5">
<PDBx:domain_id>d1kipa_</PDBx:domain_id>
<PDBx:feature>Immunoglobulin light chain kappa variable domain</PDBx:feature>
<PDBx:feature_assigned_by>SCOP</PDBx:feature_assigned_by>
<PDBx:feature_citation_id>scop</PDBx:feature_citation_id>
<PDBx:feature_name>domain</PDBx:feature_name>
<PDBx:feature_type>value</PDBx:feature_type>
</PDBx:pdbx_feature_domain>
<PDBx:pdbx_feature_domain id="6">
<PDBx:domain_id>d1kipa_</PDBx:domain_id>
<PDBx:feature>Mouse (Mus musculus), cluster 4</PDBx:feature>
<PDBx:feature_assigned_by>SCOP</PDBx:feature_assigned_by>
<PDBx:feature_citation_id>scop</PDBx:feature_citation_id>
<PDBx:feature_name>species</PDBx:feature_name>
<PDBx:feature_type>value</PDBx:feature_type>
</PDBx:pdbx_feature_domain>
</PDBx:pdbx_feature_domainCategory>
1
1
1
1
1
1
0
1
0
1
1
1
0
1
1
1
1
pdbx_feature_domainCategory
This property indicates that datablock
has a category element pdbx_feature_domain.
pdbx_feature_domainItem
Abstract Datatype property for pdbx_feature_domain items.
reference_to_pdbx_feature_domain
cross-reference to pdbx_feature_domain
pdbx_feature_domain.domain_id
The value of attribute id in category pdbx_feature_domain references a domain
definition in category PDBX_DOMAIN.
pdbx_feature_domain.feature
The value of attribute feature_name in category pdbx_feature_domain.
pdbx_feature_domain.feature_assigned_by
attribute feature_assigned_by in category pdbx_feature_domain identifies
the individual, organization or program that
assigned the feature.
pdbx_feature_domain.feature_citation_id
attribute feature_citation_id in category pdbx_feature_domain is a
reference to a citation in the CITATION category.
pdbx_feature_domain.feature_identifier
attribute feature_identifier in category pdbx_feature_domain is an
additional identifier used to identify or
accession this feature.
pdbx_feature_domain.feature_name
attribute feature_name in category pdbx_feature_domain identifies a feature
by name.
pdbx_feature_domain.feature_software_id
attribute feature_software_id in category pdbx_feature_domain is a
reference to an application described in the
SOFTWARE category.
value
uri
attribute feature_type in category pdbx_feature_domain identifies the
type of feature.
pdbx_feature_domain.id
The value of attribute id in category pdbx_feature_domain uniquely identifies
a feature in the PDBX_FEATURE_DOMAIN category.
pdbx_feature_entry
Data items in the PDBX_FEATURE_ENTRY category records
information about properties pertaining to this
structure entry.
Example 1 - Gene Ontology data by entry
<PDBx:pdbx_feature_entryCategory>
<PDBx:pdbx_feature_entry id="1">
<PDBx:feature>DNA binding activity</PDBx:feature>
<PDBx:feature_assigned_by>GO</PDBx:feature_assigned_by>
<PDBx:feature_citation_id>GO</PDBx:feature_citation_id>
<PDBx:feature_name>molecular function</PDBx:feature_name>
<PDBx:feature_type>value</PDBx:feature_type>
</PDBx:pdbx_feature_entry>
<PDBx:pdbx_feature_entry id="2">
<PDBx:feature>regulation of transcription, DNA-dependent</PDBx:feature>
<PDBx:feature_assigned_by>GO</PDBx:feature_assigned_by>
<PDBx:feature_citation_id>GO</PDBx:feature_citation_id>
<PDBx:feature_name>biological process</PDBx:feature_name>
<PDBx:feature_type>value</PDBx:feature_type>
</PDBx:pdbx_feature_entry>
</PDBx:pdbx_feature_entryCategory>
1
1
1
1
0
1
0
1
1
1
0
1
1
1
1
pdbx_feature_entryCategory
This property indicates that datablock
has a category element pdbx_feature_entry.
pdbx_feature_entryItem
Abstract Datatype property for pdbx_feature_entry items.
reference_to_pdbx_feature_entry
cross-reference to pdbx_feature_entry
pdbx_feature_entry.feature
The value of attribute feature_name in category pdbx_feature_entry.
pdbx_feature_entry.feature_assigned_by
attribute feature_assigned_by in category pdbx_feature_entry identifies
the individual, organization or program that
assigned the feature.
pdbx_feature_entry.feature_citation_id
attribute feature_citation_id in category pdbx_feature_entry is a
reference to a citation in the CITATION category
pdbx_feature_entry.feature_identifier
attribute feature_identifier in category pdbx_feature_entry is an
additional identifier used to identify or
accession this feature.
pdbx_feature_entry.feature_name
attribute feature_name in category pdbx_feature_entry identifies a feature
by name.
pdbx_feature_entry.feature_software_id
attribute feature_software_id in category pdbx_feature_entry is a
reference to an application described in the
SOFTWARE category.
value
uri
attribute feature_type in category pdbx_feature_entry identifies the
type of feature.
pdbx_feature_entry.id
The value of attribute id in category pdbx_feature_entry uniquely identifies a
feature in the PDBX_FEATURE_ENTRY category.
pdbx_feature_monomer
Data items in the PDBX_FEATURE_MONOMER category records
information about properties pertaining to particular
monomers in this structure.
Example 1 -
<PDBx:pdbx_feature_monomerCategory>
<PDBx:pdbx_feature_monomer id="1">
<PDBx:feature>129.4</PDBx:feature>
<PDBx:feature_assigned_by>POPS</PDBx:feature_assigned_by>
<PDBx:feature_citation_id>pops</PDBx:feature_citation_id>
<PDBx:feature_name>SASA</PDBx:feature_name>
<PDBx:feature_type>value</PDBx:feature_type>
<PDBx:label_alt_id></PDBx:label_alt_id>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_comp_id>ASP</PDBx:label_comp_id>
<PDBx:label_seq_id>1</PDBx:label_seq_id>
</PDBx:pdbx_feature_monomer>
<PDBx:pdbx_feature_monomer id="1">
<PDBx:feature>35.5</PDBx:feature>
<PDBx:feature_assigned_by>POPS</PDBx:feature_assigned_by>
<PDBx:feature_citation_id>pops</PDBx:feature_citation_id>
<PDBx:feature_name>SASA</PDBx:feature_name>
<PDBx:feature_type>value</PDBx:feature_type>
<PDBx:label_alt_id></PDBx:label_alt_id>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_comp_id>ILE</PDBx:label_comp_id>
<PDBx:label_seq_id>2</PDBx:label_seq_id>
</PDBx:pdbx_feature_monomer>
<PDBx:pdbx_feature_monomer id="1">
<PDBx:feature>87.2</PDBx:feature>
<PDBx:feature_assigned_by>POPS</PDBx:feature_assigned_by>
<PDBx:feature_citation_id>pops</PDBx:feature_citation_id>
<PDBx:feature_name>SASA</PDBx:feature_name>
<PDBx:feature_type>value</PDBx:feature_type>
<PDBx:label_alt_id></PDBx:label_alt_id>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_comp_id>VAL</PDBx:label_comp_id>
<PDBx:label_seq_id>3</PDBx:label_seq_id>
</PDBx:pdbx_feature_monomer>
</PDBx:pdbx_feature_monomerCategory>
0
1
0
1
0
1
1
1
1
1
0
1
0
1
1
1
0
1
1
1
1
1
1
1
1
1
1
1
1
pdbx_feature_monomerCategory
This property indicates that datablock
has a category element pdbx_feature_monomer.
pdbx_feature_monomerItem
Abstract Datatype property for pdbx_feature_monomer items.
reference_to_pdbx_feature_monomer
cross-reference to pdbx_feature_monomer
pdbx_feature_monomer.auth_asym_id
A component of the identifier for the monomer.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_feature_monomer.auth_comp_id
A component of the identifier for the monomer.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_feature_monomer.auth_seq_id
A component of the identifier for the monomer.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_feature_monomer.feature
The value of attribute feature_name in category pdbx_feature_monomer.
pdbx_feature_monomer.feature_assigned_by
attribute feature_assigned_by in category pdbx_feature_monomer identifies
the individual, organization or program that
assigned the feature.
pdbx_feature_monomer.feature_citation_id
attribute feature_citation_id in category pdbx_feature_monomer is a
reference to a citation in the CITATION category.
pdbx_feature_monomer.feature_identifier
attribute feature_identifier in category pdbx_feature_monomer is an
additional identifier used to identify or
accession this feature.
pdbx_feature_monomer.feature_name
attribute feature_name in category pdbx_feature_monomer identifies a feature
by name.
pdbx_feature_monomer.feature_software_id
attribute feature_software_id in category pdbx_feature_monomer is a
reference to an application described in the
SOFTWARE category.
value
uri
attribute feature_type in category pdbx_feature_monomer identifies the
type of feature.
pdbx_feature_monomer.label_alt_id
A component of the identifier for the monomer.
This data item is a pointer to attribute id in category atom_sites_alt in the
ATOM_SITES_ALT category.
pdbx_feature_monomer.label_asym_id
A component of the identifier for the monomer.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_feature_monomer.label_comp_id
A component of the identifier for the monomer.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_feature_monomer.label_seq_id
A component of the identifier for the monomer.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_feature_monomer.id
The value of attribute id in category pdbx_feature_monomer uniquely identifies
a feature in the PDBX_FEATURE_MONOMER category.
pdbx_feature_sequence_range
Data items in the PDBX_FEATURE_SEQUENCE_RANGE category
records information about properties pertaining to
this structure sequence_range.
Example 1 - Secondary structure computed by program DSSP.
<PDBx:pdbx_feature_sequence_rangeCategory>
<PDBx:pdbx_feature_sequence_range id="1">
<PDBx:feature>4-helix (alpha-helix)</PDBx:feature>
<PDBx:feature_assigned_by>DSSP</PDBx:feature_assigned_by>
<PDBx:feature_name>secondary structure</PDBx:feature_name>
<PDBx:feature_software_id>DSSP</PDBx:feature_software_id>
<PDBx:feature_type>value</PDBx:feature_type>
<PDBx:seq_range_id>H1</PDBx:seq_range_id>
</PDBx:pdbx_feature_sequence_range>
<PDBx:pdbx_feature_sequence_range id="2">
<PDBx:feature>hydrogen-bonded turn in beta-ladder</PDBx:feature>
<PDBx:feature_assigned_by>DSSP</PDBx:feature_assigned_by>
<PDBx:feature_name>secondary structure</PDBx:feature_name>
<PDBx:feature_software_id>DSSP</PDBx:feature_software_id>
<PDBx:feature_type>value</PDBx:feature_type>
<PDBx:seq_range_id>T1</PDBx:seq_range_id>
</PDBx:pdbx_feature_sequence_range>
</PDBx:pdbx_feature_sequence_rangeCategory>
1
1
1
1
0
1
0
1
1
1
0
1
1
1
1
1
1
pdbx_feature_sequence_rangeCategory
This property indicates that datablock
has a category element pdbx_feature_sequence_range.
pdbx_feature_sequence_rangeItem
Abstract Datatype property for pdbx_feature_sequence_range items.
reference_to_pdbx_feature_sequence_range
cross-reference to pdbx_feature_sequence_range
pdbx_feature_sequence_range.feature
The value of attribute feature_name in category pdbx_feature_sequence_range.
pdbx_feature_sequence_range.feature_assigned_by
attribute feature_assigned_by in category pdbx_feature_sequence_range identifies
the individual, organization or program that assigned
the feature.
pdbx_feature_sequence_range.feature_citation_id
attribute feature_citation_id in category pdbx_feature_sequence_range is a
reference to a citation in the CITATION category
pdbx_feature_sequence_range.feature_identifier
attribute feature_identifier in category pdbx_feature_sequence_range is an
additional identifier used to identify or
accession this feature.
pdbx_feature_sequence_range.feature_name
attribute feature_name in category pdbx_feature_sequence_range identifies a feature
by name.
pdbx_feature_sequence_range.feature_software_id
attribute feature_software_id in category pdbx_feature_sequence_range is a
reference to an application descripted in the
SOFTWARE category.
value
uri
attribute feature_type in category pdbx_feature_sequence_range identifies the
type of feature.
pdbx_feature_sequence_range.seq_range_id
The value of attribute seq_range_id
in category pdbx_feature_sequence_range references a sequence_range definition in category
PDBX_SEQUENCE_RANGE.
pdbx_feature_sequence_range.id
The value of attribute id in category pdbx_feature_sequence_range uniquely identifies
a feature in the PDBX_FEATURE_SEQUENCE_RANGE category
pdbx_helical_symmetry
Data items in the PDBX_HELICAL_SYMMETRY category record details about the
helical symmetry group associated with this entry.
Example 1 -
<PDBx:pdbx_helical_symmetryCategory>
<PDBx:pdbx_helical_symmetry entry_id="1ABC">
<PDBx:circular_symmetry>1</PDBx:circular_symmetry>
<PDBx:dyad_axis>no</PDBx:dyad_axis>
<PDBx:n_subunits_divisor>1</PDBx:n_subunits_divisor>
<PDBx:number_of_operations>35</PDBx:number_of_operations>
<PDBx:rise_per_n_subunits>6.10</PDBx:rise_per_n_subunits>
<PDBx:rotation_per_n_subunits>131.84</PDBx:rotation_per_n_subunits>
</PDBx:pdbx_helical_symmetry>
</PDBx:pdbx_helical_symmetryCategory>
1
1
1
1
1
1
1
1
1
1
1
1
1
pdbx_helical_symmetryCategory
This property indicates that datablock
has a category element pdbx_helical_symmetry.
pdbx_helical_symmetryItem
Abstract Datatype property for pdbx_helical_symmetry items.
reference_to_pdbx_helical_symmetry
cross-reference to pdbx_helical_symmetry
pdbx_helical_symmetry.circular_symmetry
Rotational n-fold symmetry about the helical axis.
no
yes
Two-fold symmetry perpendicular to the helical axis.
pdbx_helical_symmetry.n_subunits_divisor
Number of subunits used in the calculation of rise and
rotation.
pdbx_helical_symmetry.number_of_operations
Number of operations.
pdbx_helical_symmetry.rise_per_n_subunits
Angular rotation (degrees) in N subunits
pdbx_helical_symmetry.rotation_per_n_subunits
Angular rotation (degrees) in N subunits
pdbx_helical_symmetry.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
pdbx_nmr_constraints
This section provides a tabulation of constraint data.
This example uses the data from the MCP-1 structure determination. Remember
this is a dimer so there are intersubunit constraints as well as intrasubunit
constraints.
<PDBx:pdbx_nmr_constraintsCategory>
<PDBx:pdbx_nmr_constraints entry_id="1ABC">
<PDBx:NOE_constraints_total>4458</PDBx:NOE_constraints_total>
<PDBx:NOE_intraresidue_total_count>1144</PDBx:NOE_intraresidue_total_count>
<PDBx:NOE_long_range_total_count>1356</PDBx:NOE_long_range_total_count>
<PDBx:NOE_medium_range_total_count>1004</PDBx:NOE_medium_range_total_count>
<PDBx:NOE_sequential_total_count>272</PDBx:NOE_sequential_total_count>
<PDBx:protein_phi_angle_constraints_total_count>96</PDBx:protein_phi_angle_constraints_total_count>
</PDBx:pdbx_nmr_constraints>
</PDBx:pdbx_nmr_constraintsCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
pdbx_nmr_constraintsCategory
This property indicates that datablock
has a category element pdbx_nmr_constraints.
pdbx_nmr_constraintsItem
Abstract Datatype property for pdbx_nmr_constraints items.
reference_to_pdbx_nmr_constraints
cross-reference to pdbx_nmr_constraints
pdbx_nmr_constraints.NA_alpha-angle_constraints_total_count
The total number of nucleic acid alpha-angle constraints used in
the final structure calculation.
18
pdbx_nmr_constraints.NA_beta-angle_constraints_total_count
The total number of nucleic acid beta-angle constraints used in
the final structure calculation.
24
pdbx_nmr_constraints.NA_chi-angle_constraints_total_count
The total number of nucleic acid chi-angle constraints used
in the final structure calculation.
15
pdbx_nmr_constraints.NA_delta-angle_constraints_total_count
The total number of nucleic acid delta-angle constraints used in
the final structure calculation.
15
pdbx_nmr_constraints.NA_epsilon-angle_constraints_total_count
The total number of nucleic acid epsilon-angle constraints used
in the final structure calculation.
31
pdbx_nmr_constraints.NA_gamma-angle_constraints_total_count
The total number of nucleic acid gamma-angle constraints used in
the final structure calculation.
12
pdbx_nmr_constraints.NA_other-angle_constraints_total_count
The total number of nucleic acid other-angle constraints used
in the final structure calculation.
5
pdbx_nmr_constraints.NA_sugar_pucker_constraints_total_count
The total number of nucleic acid sugar pucker constraints used
in the final structure calculation.
10
pdbx_nmr_constraints.NOE_constraints_total
The total number of all NOE constraints used in the final
structure calculation.
4458
pdbx_nmr_constraints.NOE_interentity_total_count
The total number of interentity, NOE constraints
used in the final structure calculation. This field should only be
if system is complex -i.e more than one entity e.g. a dimer or ligand-protein
complex
272
pdbx_nmr_constraints.NOE_interproton_distance_evaluation
Describe the method used to quantify the NOE and ROE values.
NOE buildup curves with 50, 75, 150 ms mixing times were
analyzed.
Noesy cross peak intensities were classified into three different
catagories with distances of 1.8-2.7 A, 1.8-3.5 A, 1.8- 5.0 A for strong,
medium and weak NOEs.
pdbx_nmr_constraints.NOE_intraresidue_total_count
The total number of all intraresidue, [i-j]=0, NOE constraints
used in the final structure calculation.
1144
pdbx_nmr_constraints.NOE_long_range_total_count
The total number of long range [i-j]>5 NOE constraints used
in the final structure calculation.
1356
pdbx_nmr_constraints.NOE_medium_range_total_count
The total number of medium range 1<[i-j]<=5 NOE constraints used
in the final structure calculation.
682
pdbx_nmr_constraints.NOE_motional_averaging_correction
Describe any corrections that were made to the NOE data for motional averaging.
Replace with item example text
pdbx_nmr_constraints.NOE_pseudoatom_corrections
Describe any corrections made for pseudoatoms
Pseudo-atoms nomenclature and corrections according to Wuethrich, Billeter,
and Braun, J. Mol.Biol.(1983) 169, 949-961.
Pseudoatoms were not used.
pdbx_nmr_constraints.NOE_sequential_total_count
The total number of sequential, [i-j]=1, NOE constraints used
in the final structure calculation.
1004
pdbx_nmr_constraints.disulfide_bond_constraints_total_count
The total number of disulfide bond constraints used in the final
structure calculation.
3
pdbx_nmr_constraints.hydrogen_bond_constraints_total_count
The total number of hydrogen bond constraints used in the final
structure calculation.
6
pdbx_nmr_constraints.protein_chi_angle_constraints_total_count
The total number of chi angle constraints used in the final structure
calculation.
66
pdbx_nmr_constraints.protein_other_angle_constraints_total_count
The total number of other angle constraints used in the final structure
calculation.
0
pdbx_nmr_constraints.protein_phi_angle_constraints_total_count
The total number of phi angle constraints used in the final structure
calculation
96
pdbx_nmr_constraints.protein_psi_angle_constraints_total_count
The total number of psi angle constraints used in the final structure
calculation.
0
pdbx_nmr_constraints.entry_id
You can leave this blank as an ID will be assigned by the MSD
to the constraint file.
pdbx_nmr_details
Experimental details of the NMR study that have not been
described elsewhere in this deposition.
0
1
1
pdbx_nmr_detailsCategory
This property indicates that datablock
has a category element pdbx_nmr_details.
pdbx_nmr_detailsItem
Abstract Datatype property for pdbx_nmr_details items.
reference_to_pdbx_nmr_details
cross-reference to pdbx_nmr_details
pdbx_nmr_details.text
Additional details describing the NMR experiment.
This structure was determined using standard 2D homonuclear techniques.
The structure was determined using triple-resonance NMR spectroscopy.
pdbx_nmr_details.entry_id
The entry ID for the structure determination.
pdbx_nmr_ensemble
This category contains the information that describes the
ensemble of deposited structures. If only an average structure
has been deposited skip this section.
This example uses the data from the MCP-1 study.
<PDBx:pdbx_nmr_ensembleCategory>
<PDBx:pdbx_nmr_ensemble entry_id="1ABC">
<PDBx:conformer_selection_criteria>structures with the least restraint violations</PDBx:conformer_selection_criteria>
<PDBx:conformers_calculated_total_number>40</PDBx:conformers_calculated_total_number>
<PDBx:conformers_submitted_total_number>20</PDBx:conformers_submitted_total_number>
<PDBx:representative_conformer>1</PDBx:representative_conformer>
</PDBx:pdbx_nmr_ensemble>
</PDBx:pdbx_nmr_ensembleCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
pdbx_nmr_ensembleCategory
This property indicates that datablock
has a category element pdbx_nmr_ensemble.
pdbx_nmr_ensembleItem
Abstract Datatype property for pdbx_nmr_ensemble items.
reference_to_pdbx_nmr_ensemble
cross-reference to pdbx_nmr_ensemble
pdbx_nmr_ensemble.average_constraint_violations_per_residue
The average number of constraint violations on a per residue basis for
the ensemble.
0.25
pdbx_nmr_ensemble.average_constraints_per_residue
The average number of constraints per residue for the ensemble
30.2
pdbx_nmr_ensemble.average_distance_constraint_violation
The average distance restraint violation for the ensemble.
0.11
pdbx_nmr_ensemble.average_torsion_angle_constraint_violation
The average torsion angle constraint violation for the ensemble.
2.4
pdbx_nmr_ensemble.conformer_selection_criteria
By highlighting the appropriate choice(s), describe how the submitted
conformer (models) were selected.
structures with the lowest energy
structures with the least restraint violations
structures with acceptable covalent geometry
structures with favorable non-bond energy
target function
back calculated data agree with experimental NOESY spectrum
all calculated structures submitted
The submitted conformer models are the 25 structures with the lowest
energy.
The submitted conformer models are those with the fewest number of
constraint violations.
pdbx_nmr_ensemble.conformers_calculated_total_number
The total number of conformer (models) that were calculated in the final round.
40
pdbx_nmr_ensemble.conformers_submitted_total_number
The number of conformer (models) that are submitted for the ensemble.
20
pdbx_nmr_ensemble.distance_constraint_violation_method
Describe the method used to calculate the distance constraint violation statistics,
i.e. are they calculated over all the distance constraints or calculated for
violations only?
Statistics were calculated over all of the distance constraints.
Statistics were calculated for violations only
pdbx_nmr_ensemble.maximum_distance_constraint_violation
The maximum distance constraint violation for the ensemble.
0.4
pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation
The maximum lower distance constraint violation for the ensemble.
0.3
pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation
The maximum torsion angle constraint violation for the ensemble.
4
pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation
The maximum upper distance constraint violation for the ensemble.
0.4
pdbx_nmr_ensemble.representative_conformer
The number of the conformer identified as most representative.
20
pdbx_nmr_ensemble.torsion_angle_constraint_violation_method
This item describes the method used to calculate the torsion angle constraint violation statistics.
i.e. are the entered values based on all torsion angle or calculated for violations only?
Statistics were calculated over all the torsion angle constraints.
Statistics were calculated for torsion angle constraints violations only.
pdbx_nmr_ensemble.entry_id
Leave this blank as the ID is provided by the MSD
pdbx_nmr_ensemble_rms
Structural statistics are derived from molecular dynamics and simulated annealing
programs.
This example is derived from the MCP-1 structure calculation statistics.
For this structure the statistics were calculated over residues 5-69 for
both the monomer and dimer .
<PDBx:pdbx_nmr_ensemble_rmsCategory>
<PDBx:pdbx_nmr_ensemble_rms entry_id="1ABC">
<PDBx:atom_type>all heavy atoms</PDBx:atom_type>
<PDBx:chain_range_begin>A</PDBx:chain_range_begin>
<PDBx:chain_range_end>A</PDBx:chain_range_end>
<PDBx:distance_rms_dev>0.22</PDBx:distance_rms_dev>
<PDBx:distance_rms_dev_error>0.06</PDBx:distance_rms_dev_error>
<PDBx:residue_range_begin>5</PDBx:residue_range_begin>
<PDBx:residue_range_end>69</PDBx:residue_range_end>
</PDBx:pdbx_nmr_ensemble_rms>
</PDBx:pdbx_nmr_ensemble_rmsCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
pdbx_nmr_ensemble_rmsCategory
This property indicates that datablock
has a category element pdbx_nmr_ensemble_rms.
pdbx_nmr_ensemble_rmsItem
Abstract Datatype property for pdbx_nmr_ensemble_rms items.
reference_to_pdbx_nmr_ensemble_rms
cross-reference to pdbx_nmr_ensemble_rms
backbone heavy atoms
side chain heavy atoms
all heavy atoms
all atoms
all backbone atoms
Statistics are often calculated over only some of the atoms,
e.g. backbone, or heavy atoms. Describe which type of atoms are used for
the statistical analysis.
backbone atoms
heavy atoms
pdbx_nmr_ensemble_rms.bond_angle_rms_dev
The bond angle rmsd to the target values for the ensemble.
0.60
pdbx_nmr_ensemble_rms.bond_angle_rms_dev_error
The error in the bond angle rmsd.
0.01
pdbx_nmr_ensemble_rms.chain_range_begin
The beginning chain id.
A
pdbx_nmr_ensemble_rms.chain_range_end
The ending chain id:
A
pdbx_nmr_ensemble_rms.coord_average_rmsd_method
Describe the method for calculating the coordinate average rmsd.
Replace with item example text
pdbx_nmr_ensemble_rms.covalent_bond_rms_dev
The covalent bond rmsd to the target value for the ensemble.
0.0066
pdbx_nmr_ensemble_rms.covalent_bond_rms_dev_error
The error in the covalent bond rmsd.
0.0001
pdbx_nmr_ensemble_rms.dihedral_angles_rms_dev
The dihedral angle rmsd to the target values for the ensemble.
0.66
pdbx_nmr_ensemble_rms.dihedral_angles_rms_dev_error
The error of the rmsd dihedral angles.
0.07
pdbx_nmr_ensemble_rms.distance_rms_dev
The distance rmsd to the mean structure for the ensemble of structures.
0.22
pdbx_nmr_ensemble_rms.distance_rms_dev_error
The error in the distance rmsd.
0.07
pdbx_nmr_ensemble_rms.improper_torsion_angle_rms_dev
The improper torsion angle rmsd to the target values for the ensemble.
0.64
pdbx_nmr_ensemble_rms.improper_torsion_angle_rms_dev_error
The error in the improper torsion angle rmsd.
0.04
pdbx_nmr_ensemble_rms.peptide_planarity_rms_dev
The peptide planarity rmsd.
0.11
pdbx_nmr_ensemble_rms.peptide_planarity_rms_dev_error
The error in the peptide planarity rmsd.
0.05
pdbx_nmr_ensemble_rms.residue_range_begin
Structure statistics are often calculated only over the well-ordered region(s)
of the biopolymer. Portions of the macromolecule are often mobile and
disordered, hence they are excluded in calculating the statistics. To define
the range(s) over which the statistics are calculated, enter the beginning
residue number(s): e.g. if the regions used were 5-32 and 41-69, enter 5,41
5
41
pdbx_nmr_ensemble_rms.residue_range_end
The ending residue number: e.g. 32,69.
32
69
pdbx_nmr_ensemble_rms.entry_id
'?'
pdbx_nmr_exptl
In this section, enter information on those experiments that were
used to generate constraint data. For each NMR experiment indicate
which sample and which sample conditions were used for the experiment.
This example was taken from the MCP-1 study.
<PDBx:pdbx_nmr_exptlCategory>
<PDBx:pdbx_nmr_exptl conditions_id="1" experiment_id="1" solution_id="3">
<PDBx:type>3D_15N-separated_NOESY</PDBx:type>
</PDBx:pdbx_nmr_exptl>
<PDBx:pdbx_nmr_exptl conditions_id="1" experiment_id="2" solution_id="1">
<PDBx:type>3D_13C-separated_NOESY</PDBx:type>
</PDBx:pdbx_nmr_exptl>
<PDBx:pdbx_nmr_exptl conditions_id="2" experiment_id="3" solution_id="1">
<PDBx:type>4D_13C/15N-separated_NOESY</PDBx:type>
</PDBx:pdbx_nmr_exptl>
<PDBx:pdbx_nmr_exptl conditions_id="1" experiment_id="4" solution_id="1">
<PDBx:type>4D_13C-separated_NOESY</PDBx:type>
</PDBx:pdbx_nmr_exptl>
<PDBx:pdbx_nmr_exptl conditions_id="1" experiment_id="5" solution_id="1">
<PDBx:type>3D_15N-separated_ROESY</PDBx:type>
</PDBx:pdbx_nmr_exptl>
<PDBx:pdbx_nmr_exptl conditions_id="1" experiment_id="6" solution_id="3">
<PDBx:type>3D_13C-separated_ROESY</PDBx:type>
</PDBx:pdbx_nmr_exptl>
</PDBx:pdbx_nmr_exptlCategory>
0
1
1
1
1
pdbx_nmr_exptlCategory
This property indicates that datablock
has a category element pdbx_nmr_exptl.
pdbx_nmr_exptlItem
Abstract Datatype property for pdbx_nmr_exptl items.
reference_to_pdbx_nmr_exptl
cross-reference to pdbx_nmr_exptl
pdbx_nmr_exptl.type
The type of NMR experiment.
2D NOESY
3D_15N-separated_NOESY
3D_13C-separated_NOESY
4D_13C-separated_NOESY
4D_13C/15N-separated_NOESY
3D_15N-separated_ROESY
3D_13C-separated_ROESY
HNCA-J
HNHA
DQF-COSY
P-COSY
PE-COSY
E-COSY
pdbx_nmr_exptl.conditions_id
The number to identify the set of sample conditions.
1
2
3
pdbx_nmr_exptl.experiment_id
A numerical ID for each experiment.
1
2
3
pdbx_nmr_exptl.solution_id
The solution_id from the Experimental Sample to identify the sample
that these conditions refer to.
[Remember to save the entries here before returning to the
Experimental Sample form]
1
2
3
pdbx_nmr_exptl_sample
The chemical constituents of
each NMR sample. Each sample is identified by a number and
each component in the sample is identified by name.
Example 1
This example was taken from the study of MCP-1 which is a dimer under the
conditions studied. Three solutions with different isotope compositions were
studied.
<PDBx:pdbx_nmr_exptl_sampleCategory>
<PDBx:pdbx_nmr_exptl_sample component="MCP-1" solution_id="1">
<PDBx:concentration>2</PDBx:concentration>
<PDBx:concentration_units>mM</PDBx:concentration_units>
<PDBx:isotopic_labeling>U-15N,13C</PDBx:isotopic_labeling>
</PDBx:pdbx_nmr_exptl_sample>
<PDBx:pdbx_nmr_exptl_sample component="H2O" solution_id="1">
<PDBx:concentration>90</PDBx:concentration>
<PDBx:concentration_units>%</PDBx:concentration_units>
<PDBx:isotopic_labeling></PDBx:isotopic_labeling>
</PDBx:pdbx_nmr_exptl_sample>
<PDBx:pdbx_nmr_exptl_sample component="D2O" solution_id="1">
<PDBx:concentration>10</PDBx:concentration>
<PDBx:concentration_units>%</PDBx:concentration_units>
<PDBx:isotopic_labeling></PDBx:isotopic_labeling>
</PDBx:pdbx_nmr_exptl_sample>
</PDBx:pdbx_nmr_exptl_sampleCategory>
Example 2
This example was taken from the study of MCP-1 which is a dimer under the
conditions studied. Three solutions with different isotope compositions were
studied.
<PDBx:pdbx_nmr_exptl_sampleCategory>
<PDBx:pdbx_nmr_exptl_sample component="MCP-1" solution_id="2">
<PDBx:concentration>1</PDBx:concentration>
<PDBx:concentration_units>mM</PDBx:concentration_units>
<PDBx:isotopic_labeling>U-50% 15N</PDBx:isotopic_labeling>
</PDBx:pdbx_nmr_exptl_sample>
<PDBx:pdbx_nmr_exptl_sample component="H2O" solution_id="2">
<PDBx:concentration>90</PDBx:concentration>
<PDBx:concentration_units>%</PDBx:concentration_units>
<PDBx:isotopic_labeling></PDBx:isotopic_labeling>
</PDBx:pdbx_nmr_exptl_sample>
<PDBx:pdbx_nmr_exptl_sample component="D2O" solution_id="2">
<PDBx:concentration>10</PDBx:concentration>
<PDBx:concentration_units>%</PDBx:concentration_units>
<PDBx:isotopic_labeling></PDBx:isotopic_labeling>
</PDBx:pdbx_nmr_exptl_sample>
</PDBx:pdbx_nmr_exptl_sampleCategory>
0
1
0
1
0
1
0
1
1
1
pdbx_nmr_exptl_sampleCategory
This property indicates that datablock
has a category element pdbx_nmr_exptl_sample.
pdbx_nmr_exptl_sampleItem
Abstract Datatype property for pdbx_nmr_exptl_sample items.
reference_to_pdbx_nmr_exptl_sample
cross-reference to pdbx_nmr_exptl_sample
pdbx_nmr_exptl_sample.concentration
The concentration value of the component.
2.0
2.7
0.01
pdbx_nmr_exptl_sample.concentration_range
The concentration range for the component.
2.0-2.2
2.7-3.5
0.01-0.05
%
mM
mg/mL
M
g/L
uM
v/v
w/v
The concentration units of the component.
mg/mL for mg per milliliter
mM for millimolar
% for percent by volume
pdbx_nmr_exptl_sample.isotopic_labeling
The isotopic composition of each component, including
the % labeling level, if known. For example:
1. Uniform (random) labeling with 15N: U-15N
2. Uniform (random) labeling with 13C, 15N at known labeling
levels: U-95% 13C;U-98% 15N
3. Residue selective labeling: U-95% 15N-Thymine
4. Site specific labeling: 95% 13C-Ala18,
5. Natural abundance labeling in an otherwise uniformly labled
biomolecule is designated by NA: U-13C; NA-K,H
U-13C,15N
U-2H
pdbx_nmr_exptl_sample.component
The name of each component in the sample
ribonuclease
DNA strand 1
TRIS buffer
sodium chloride
H2O
D2O
pdbx_nmr_exptl_sample.solution_id
The name (number) of the sample.
1
2
3
pdbx_nmr_exptl_sample_conditions
The experimental conditions used to for each sample. Each set of conditions
is identified by a numerical code.
This example was taken from a pH stability study.
<PDBx:pdbx_nmr_exptl_sample_conditionsCategory>
<PDBx:pdbx_nmr_exptl_sample_conditions conditions_id="1">
<PDBx:ionic_strength>25mM NaCl</PDBx:ionic_strength>
<PDBx:pH>7</PDBx:pH>
<PDBx:pressure>ambient</PDBx:pressure>
<PDBx:temperature>298</PDBx:temperature>
</PDBx:pdbx_nmr_exptl_sample_conditions>
<PDBx:pdbx_nmr_exptl_sample_conditions conditions_id="2">
<PDBx:ionic_strength>25mM NaCl</PDBx:ionic_strength>
<PDBx:pH>3</PDBx:pH>
<PDBx:pressure>ambient</PDBx:pressure>
<PDBx:temperature>298</PDBx:temperature>
</PDBx:pdbx_nmr_exptl_sample_conditions>
</PDBx:pdbx_nmr_exptl_sample_conditionsCategory>
0
1
0
1
0
1
0
1
0
1
1
pdbx_nmr_exptl_sample_conditionsCategory
This property indicates that datablock
has a category element pdbx_nmr_exptl_sample_conditions.
pdbx_nmr_exptl_sample_conditionsItem
Abstract Datatype property for pdbx_nmr_exptl_sample_conditions items.
reference_to_pdbx_nmr_exptl_sample_conditions
cross-reference to pdbx_nmr_exptl_sample_conditions
pdbx_nmr_exptl_sample_conditions.ionic_strength
The ionic strength at which the NMR data were collected -in lieu of
this enter the concentration and identity of the salt in the sample.
pdbx_nmr_exptl_sample_conditions.pH
The pH at which the NMR data were collected.
3.1
7.0
pdbx_nmr_exptl_sample_conditions.pressure
The pressure at which NMR data were collected.
ambient
1atm
pdbx_nmr_exptl_sample_conditions.pressure_units
The units of pressure at which NMR data were collected.
Pa
atm
Torr
pdbx_nmr_exptl_sample_conditions.temperature
The temperature (in Kelvin) at which NMR data were
collected.
298
pdbx_nmr_exptl_sample_conditions.conditions_id
The condition number as defined above.
1
2
3
pdbx_nmr_force_constants
The final force constants, including units, employed for the various
experimental constraints, covalent geometry constraints, and the non-bonded
interaction terms in the target function used for simulated annealing.
This example is taken from a study of BAF, a dimeric DNA binding protein.
The final force constants in the target function used for simulated
annealing are: Experimental Constraint terms: Distance (NOE,H-bonds),
Torsion angles, J coupling, 13C shifts, 1H shifts, Dipolar coupling,
D isotope shifts Covalent Geometry Constraint terms: Bond lengths,
Angles, Impropers Non-bonded Interaction terms: van der Waals,
Type of van der Waals term, Conformational database potential,
Radius of gyration.
<PDBx:pdbx_nmr_force_constantsCategory>
<PDBx:pdbx_nmr_force_constants entry_id="1ABC">
<PDBx:covalent_geom_bond_term>1000.</PDBx:covalent_geom_bond_term>
<PDBx:covalent_geom_bond_term_units>kcal/mol/A**2</PDBx:covalent_geom_bond_term_units>
<PDBx:exptl_13C_shift_term>0.5</PDBx:exptl_13C_shift_term>
<PDBx:exptl_13C_shift_term_units>kcal/mol/ppm**2</PDBx:exptl_13C_shift_term_units>
<PDBx:exptl_1H_shift_term>7.5</PDBx:exptl_1H_shift_term>
<PDBx:exptl_1H_shift_term_units>kcal/mol/ppm**2</PDBx:exptl_1H_shift_term_units>
<PDBx:exptl_J_coupling_term>1.</PDBx:exptl_J_coupling_term>
<PDBx:exptl_J_coupling_term_units>kcal/mol/Hz**2</PDBx:exptl_J_coupling_term_units>
<PDBx:exptl_distance_term>30.</PDBx:exptl_distance_term>
<PDBx:exptl_distance_term_units>kcal/mol/A**2</PDBx:exptl_distance_term_units>
<PDBx:exptl_torsion_angles_term>200.</PDBx:exptl_torsion_angles_term>
<PDBx:exptl_torsion_angles_term_units>kcal/mol/rad**2</PDBx:exptl_torsion_angles_term_units>
<PDBx:non-bonded_inter_van_der_Waals_term_type>4.</PDBx:non-bonded_inter_van_der_Waals_term_type>
<PDBx:non-bonded_inter_van_der_Waals_term_units>kcal/mol/A**4</PDBx:non-bonded_inter_van_der_Waals_term_units>
</PDBx:pdbx_nmr_force_constants>
</PDBx:pdbx_nmr_force_constantsCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
pdbx_nmr_force_constantsCategory
This property indicates that datablock
has a category element pdbx_nmr_force_constants.
pdbx_nmr_force_constantsItem
Abstract Datatype property for pdbx_nmr_force_constants items.
reference_to_pdbx_nmr_force_constants
cross-reference to pdbx_nmr_force_constants
pdbx_nmr_force_constants.covalent_geom_angles_term
The final force constant for covalent geometry angle constraints
term employed in the target function used for simulated annealing.
500
kcal/mol/rad**2
kJ/mol/rad**2
other
The units for the force constant for the covalent geometry angle
constraints term.
kcal/mol/rad**2
pdbx_nmr_force_constants.covalent_geom_bond_term
The final force constant for the covalent geometry bond length
constraints term employed in the target function used for simulated
annealing.
1000
kcal/mol/A**2
kJ/mol/nm**2
other
The units for the force constant for the covalent geometry bond
length constraints term.
kcal/mol/A**2
pdbx_nmr_force_constants.covalent_geom_impropers_term
The final force constant for covalent geometry impropers
contstraints term employed in the target function used for simulated
annealing.
500
kcal/mol/rad**2
kJ/mol/rad**2
other
The units for the force constant for the covalent geometry
impropers constraints term.
kcal/mol/rad**2
pdbx_nmr_force_constants.exptl_13C_shift_term
The final force constant for 13C shift constraints term employed
in the target function used for simulated annealing.
0.5
kcal/mol/ppm**2
kJ/mol/ppm**2
other
The units for the force constant for the 13C shift constraints
term.
kcal/mol/ppm**2
pdbx_nmr_force_constants.exptl_1H_shift_term
The final force constant for 1H shift constraints term employed
in the target function used for simulated annealing.
7.5
kcal/mol/ppm**2
kJ/mol/ppm**2
other
The units for the force constant for the 1H shift constraints term.
kcal/mol/ppm**2
pdbx_nmr_force_constants.exptl_D_isotope_shift_term
The final force constant for Deuterium isotope shift constraints
term employed in the target function used for simulated annealing.
0.5
kcal/mol/ppb**2
kJ/mol/ppb**2
other
The units for the force constant for the Deuterium isotope
shift constraints term.
kcal/mol/ppb**2
pdbx_nmr_force_constants.exptl_J_coupling_term
The final force constant for J coupling term employed in the
target function used for simulated annealing.
1
kcal/mol/Hz**2
kJ/mol/Hz**2
other
The units for the force constant for the J coupling term.
kcal/mol/Hz**2
pdbx_nmr_force_constants.exptl_dipolar_coupling_term
The final force constant for dipolar coupling constraint term
employed in the target function used for simulated annealing.
1
kcal/mol/Hz**2
kJ/mol/Hz**2
other
The units for the force constant for the dipolar coupling
constraints term.
kcal/mol/Hz**2
pdbx_nmr_force_constants.exptl_distance_term
The final force constant for distance (NOEs) constraints
term employed in the target function used for simulated annealing.
30
kcal/mol/A**2
kJ/mol/nm**2
other
The units for the force constant for the distance
constraints term.
kcal/mol/ A**2
pdbx_nmr_force_constants.exptl_torsion_angles_term
The final force constant for the torsion angle term employed in
the target function used for simulated annealing.
200
kcal/mol/rad**2
kJ/mol/rad**2
author
The units for the force constant for the torsion angle
constraints term.
kcal/mol/rad**2
pdbx_nmr_force_constants.non-bonded_inter_conf_db_potential_term
The force constant used for the non-bonded interaction conformational
database potential term employed in the target function used for simulated
annealing.
1.0
pdbx_nmr_force_constants.non-bonded_inter_radius_of_gyration_term
The force constant used for the non-bonded interaction radius of
gyration term employed in the target function used for simulated annealing.
100
kcal/mol/ A**2
kJ/mol/ nm**4
other
The units for the force constant for the radius of gyration term.
kcal/mol/ A**2
pdbx_nmr_force_constants.non-bonded_inter_van_der_Waals_term
The force constant used for the non-bonded interaction van der Waals
term employed in the target function used for simulated annealing.
4
quartic
other
The type of van der Waals term employed in the target function
used for simulated annealing.
quartic
kcal/mol/A**4
kJ/mol/nm**4
other
The units for the force constant for the van der Waals term.
kcal/mol/ A**4
pdbx_nmr_force_constants.entry_id
You can leave this blank as an ID will be assigned by the RCSB.
pdbx_nmr_refine
Describe the method and details of the refinement of the deposited structure.
This example is drawn from the MCP-1 structure.
<PDBx:pdbx_nmr_refineCategory>
<PDBx:pdbx_nmr_refine entry_id="1ABC">
<PDBx:method>torsion angle dynamics</PDBx:method>
</PDBx:pdbx_nmr_refine>
</PDBx:pdbx_nmr_refineCategory>
0
1
0
1
1
pdbx_nmr_refineCategory
This property indicates that datablock
has a category element pdbx_nmr_refine.
pdbx_nmr_refineItem
Abstract Datatype property for pdbx_nmr_refine items.
reference_to_pdbx_nmr_refine
cross-reference to pdbx_nmr_refine
pdbx_nmr_refine.details
Additional details about the NMR refinement.
Additional comments about the NMR refinement can be placed here, e.g.
the structures are based on a total of 3344 restraints, 3167 are NOE-derived
distance constraints, 68 dihedral angle restraints,109 distance restraints
from hydrogen bonds.
pdbx_nmr_refine.method
The method used to determine the structure.
distance geometry
simulated annealing
molecular dynamics
matrix relaxation
torsion angle dynamics
pdbx_nmr_refine.entry_id
You can leave this blank as an ID will be assigned by the RCSB
to the constraint file.
pdbx_nmr_representative
An average structure is often calculated in addition to the ensemble, or one
of the ensemble is selected as a representative structure. This section
describes selection of the representative structure.
This example is drawn from the MCP-1 structure.
<PDBx:pdbx_nmr_representativeCategory>
<PDBx:pdbx_nmr_representative entry_id="1ABC">
<PDBx:conformer_id>15</PDBx:conformer_id>
<PDBx:selection_criteria>lowest energy</PDBx:selection_criteria>
</PDBx:pdbx_nmr_representative>
</PDBx:pdbx_nmr_representativeCategory>
0
1
0
1
1
pdbx_nmr_representativeCategory
This property indicates that datablock
has a category element pdbx_nmr_representative.
pdbx_nmr_representativeItem
Abstract Datatype property for pdbx_nmr_representative items.
reference_to_pdbx_nmr_representative
cross-reference to pdbx_nmr_representative
pdbx_nmr_representative.conformer_id
If a member of the ensemble has been selected as a representative
structure, identify it by its model number.
15
pdbx_nmr_representative.selection_criteria
By highlighting the appropriate choice(s), describe the criteria used to
select this structure as a representative structure, or if an average
structure has been calculated describe how this was done.
The structure closest to the average.
The structure with the lowest energy was selected.
The structure with the fewest number of violations was selected.
A minimized average structure was calculated.
pdbx_nmr_representative.entry_id
msd will assign the ID.
pdbx_nmr_sample_details
Complete description of each NMR sample, including the solvent
system used.
This example was taken from the study of MCP-1 which is a dimer under the
conditions studied. Three solutions with different isotope compositions were
studied.
<PDBx:pdbx_nmr_sample_detailsCategory>
<PDBx:pdbx_nmr_sample_details solution_id="1">
<PDBx:contents>2 mM U-15N,13C, H2O 90 %, D2O 10 %</PDBx:contents>
<PDBx:solvent_system>MCP-1</PDBx:solvent_system>
</PDBx:pdbx_nmr_sample_details>
<PDBx:pdbx_nmr_sample_details solution_id="2">
<PDBx:contents>1 mM U-50% 15N, MCP-1 1 mM U-50% 13C, H2O 90 %, D2O 10 %</PDBx:contents>
<PDBx:solvent_system>MCP-1</PDBx:solvent_system>
</PDBx:pdbx_nmr_sample_details>
<PDBx:pdbx_nmr_sample_details solution_id="3">
<PDBx:contents>2 mM U-15N, H2O 90 %, D2O 10 %</PDBx:contents>
<PDBx:solvent_system>MCP-1</PDBx:solvent_system>
</PDBx:pdbx_nmr_sample_details>
</PDBx:pdbx_nmr_sample_detailsCategory>
0
1
0
1
1
pdbx_nmr_sample_detailsCategory
This property indicates that datablock
has a category element pdbx_nmr_sample_details.
pdbx_nmr_sample_detailsItem
Abstract Datatype property for pdbx_nmr_sample_details items.
reference_to_pdbx_nmr_sample_details
cross-reference to pdbx_nmr_sample_details
pdbx_nmr_sample_details.contents
A complete description of each NMR sample. Include the concentration
and concentration units for each component (include buffers, etc.). For each
component describe the isotopic composition, including the % labeling level,
if known.
For example:
1. Uniform (random) labeling with 15N: U-15N
2. Uniform (random) labeling with 13C, 15N at known labeling
levels: U-95% 13C;U-98% 15N
3. Residue selective labeling: U-95% 15N-Thymine
4. Site specific labeling: 95% 13C-Ala18,
5. Natural abundance labeling in an otherwise uniformly labeled
biomolecule is designated by NA: U-13C; NA-K,H
2mM Ribonuclease U-15N,13C; 50mM phosphate buffer NA; 90% H2O, 10% D2O
pdbx_nmr_sample_details.solvent_system
The solvent system used for this sample.
90% H2O, 10% D2O
pdbx_nmr_sample_details.solution_id
The name (number) of the sample.
1
2
3
pdbx_nmr_software
Description of the software that was used for data collection, data processing,
data analysis, structure calculations and refinement. The description should
include the name of the software, the author of the software and the version used.
This example describes the software used in the MCP-1 study.
<PDBx:pdbx_nmr_softwareCategory>
<PDBx:pdbx_nmr_software ordinal="1">
<PDBx:authors>Bruker</PDBx:authors>
<PDBx:classification>collection</PDBx:classification>
<PDBx:name>UXNMR</PDBx:name>
<PDBx:version>940501.3</PDBx:version>
</PDBx:pdbx_nmr_software>
<PDBx:pdbx_nmr_software ordinal="2">
<PDBx:authors>Hare</PDBx:authors>
<PDBx:classification>processing</PDBx:classification>
<PDBx:name>FELIX</PDBx:name>
<PDBx:version>1.1</PDBx:version>
</PDBx:pdbx_nmr_software>
<PDBx:pdbx_nmr_software ordinal="3">
<PDBx:authors>Kraulis</PDBx:authors>
<PDBx:classification>data analysis</PDBx:classification>
<PDBx:name>ANSIG</PDBx:name>
<PDBx:version>3.0</PDBx:version>
</PDBx:pdbx_nmr_software>
<PDBx:pdbx_nmr_software ordinal="4">
<PDBx:authors>Brunger</PDBx:authors>
<PDBx:classification>structure calculation</PDBx:classification>
<PDBx:name>X-PLOR</PDBx:name>
<PDBx:version>3.8</PDBx:version>
</PDBx:pdbx_nmr_software>
</PDBx:pdbx_nmr_softwareCategory>
0
1
1
1
1
1
0
1
1
pdbx_nmr_softwareCategory
This property indicates that datablock
has a category element pdbx_nmr_software.
pdbx_nmr_softwareItem
Abstract Datatype property for pdbx_nmr_software items.
reference_to_pdbx_nmr_software
cross-reference to pdbx_nmr_software
pdbx_nmr_software.authors
The name of the authors of the software used in this
procedure.
Brunger
Guentert
pdbx_nmr_software.classification
The purpose of the software.
collection
processing
data analysis
structure solution
refinement
iterative matrix relaxation
pdbx_nmr_software.name
The name of the software used for the task.
ANSIG
AURELIA
AZARA
CHARMM
CORMA
DIANA
DYANA
DSPACE
DISGEO
DGII
DISMAN
DINOSAUR
DISCOVER
FELIX
FT_NMR
GROMOS
IRMA
MARDIGRAS
NMRPipe
SA
UXNMR
VNMR
X-PLOR
XWINNMR
pdbx_nmr_software.version
The version of the software.
940501.3
2.1
pdbx_nmr_software.ordinal
An ordinal index for this category
1
2
pdbx_nmr_spectrometer
The details about each spectrometer used to collect data for this
deposition.
The instruments described here are the ones used for the MCP-1 studies.
<PDBx:pdbx_nmr_spectrometerCategory>
<PDBx:pdbx_nmr_spectrometer spectrometer_id="1">
<PDBx:field_strength>600</PDBx:field_strength>
<PDBx:type>Bruker AMX</PDBx:type>
</PDBx:pdbx_nmr_spectrometer>
<PDBx:pdbx_nmr_spectrometer spectrometer_id="2">
<PDBx:field_strength>500</PDBx:field_strength>
<PDBx:type>Bruker AMX</PDBx:type>
</PDBx:pdbx_nmr_spectrometer>
</PDBx:pdbx_nmr_spectrometerCategory>
0
1
0
1
0
1
0
1
1
pdbx_nmr_spectrometerCategory
This property indicates that datablock
has a category element pdbx_nmr_spectrometer.
pdbx_nmr_spectrometerItem
Abstract Datatype property for pdbx_nmr_spectrometer items.
reference_to_pdbx_nmr_spectrometer
cross-reference to pdbx_nmr_spectrometer
pdbx_nmr_spectrometer.field_strength
Select the field strength for protons in MHz.
360
400
500
600
750
800
850
900
950
1000
pdbx_nmr_spectrometer.manufacturer
The name of the manufacturer of the spectrometer.
Varian
Bruker
JEOL
GE
pdbx_nmr_spectrometer.model
The model of the NMR spectrometer.
AVANCE
WH
WM
AM
AMX
DMX
DRX
MSL
OMEGA
OMEGA PSG
GX
GSX
A
AL
EC
EX
LA
ECP
VXRS
UNITY
UNITYPLUS
INOVA
pdbx_nmr_spectrometer.type
Select the instrument manufacturer(s) and the model(s) of the NMR(s)
used for this work.
Bruker WH
Bruker WM
Bruker AM
Bruker AMX
Bruker DMX
Bruker DRX
Bruker MSL
Bruker AVANCE
GE Omega
GE Omega PSG
JEOL GX
JEOL GSX
JEOL A
JEOL AL
JEOL EC
JEOL EX
JEOL LA
JEOL ECP
Varian VXRS
Varian UNITY
Varian UNITYplus
Varian INOVA
other
pdbx_nmr_spectrometer.spectrometer_id
Assign a numerical ID to each instrument.
1
2
3
pdbx_nonpoly_scheme
The PDBX_NONPOLY_SCHEME category provides residue level nomenclature
mapping for non-polymer entities.
Example 1 -
<PDBx:pdbx_nonpoly_schemeCategory>
<PDBx:pdbx_nonpoly_scheme asym_id="C" ndb_seq_num="100">
<PDBx:auth_mon_id>HOH</PDBx:auth_mon_id>
<PDBx:auth_seq_num>100</PDBx:auth_seq_num>
<PDBx:entity_id>3</PDBx:entity_id>
<PDBx:mon_id>HOH</PDBx:mon_id>
<PDBx:pdb_ins_code></PDBx:pdb_ins_code>
<PDBx:pdb_mon_id>HOH</PDBx:pdb_mon_id>
<PDBx:pdb_seq_num>100</PDBx:pdb_seq_num>
<PDBx:pdb_strand_id>C</PDBx:pdb_strand_id>
</PDBx:pdbx_nonpoly_scheme>
</PDBx:pdbx_nonpoly_schemeCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
pdbx_nonpoly_schemeCategory
This property indicates that datablock
has a category element pdbx_nonpoly_scheme.
pdbx_nonpoly_schemeItem
Abstract Datatype property for pdbx_nonpoly_scheme items.
reference_to_pdbx_nonpoly_scheme
cross-reference to pdbx_nonpoly_scheme
pdbx_nonpoly_scheme.auth_mon_id
attribute auth_comp_id in category atom_site
pdbx_nonpoly_scheme.auth_seq_num
attribute auth_seq_id in category atom_site
pdbx_nonpoly_scheme.entity_id
Pointer to attribute label_entity_id in category atom_site.
pdbx_nonpoly_scheme.mon_id
Pointer to attribute label_comp_id in category atom_site.
pdbx_nonpoly_scheme.pdb_ins_code
PDB insertion code.
pdbx_nonpoly_scheme.pdb_mon_id
PDB residue name.
pdbx_nonpoly_scheme.pdb_seq_num
PDB residue number.
pdbx_nonpoly_scheme.pdb_strand_id
PDB strand/chain id.
pdbx_nonpoly_scheme.asym_id
Pointer to attribute label_asym_id in category atom_site.
1
A
2B3
pdbx_nonpoly_scheme.ndb_seq_num
NDB/RCSB residue number.
pdbx_phasing_MAD_set
Record details about each phasing set: (Note: the phasing
set is different from data set. for example: if there are
three data sets, the inflection point (IP), the peak (PK)
and the high remote (HR), the combination of the phasing
set will be IP_iso, PK_iso (the isomorphous repleacement
with HR as 'native'), IP_ano, PK_ano and HR_ano (the
anomalous difference with itself). Therefore, there are
five set used for phasing.
Example 1 - three wavelengths
<PDBx:pdbx_phasing_MAD_setCategory>
<PDBx:pdbx_phasing_MAD_set id="ISO_1">
<PDBx:R_cullis_acentric>0.000</PDBx:R_cullis_acentric>
<PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric>
<PDBx:d_res_high>2.00</PDBx:d_res_high>
<PDBx:d_res_low>22.60</PDBx:d_res_low>
<PDBx:reflns_acentric>5387</PDBx:reflns_acentric>
<PDBx:reflns_centric>471</PDBx:reflns_centric>
</PDBx:pdbx_phasing_MAD_set>
<PDBx:pdbx_phasing_MAD_set id="ISO_2">
<PDBx:R_cullis_acentric>0.803</PDBx:R_cullis_acentric>
<PDBx:R_cullis_centric>0.718</PDBx:R_cullis_centric>
<PDBx:d_res_high>2.00</PDBx:d_res_high>
<PDBx:d_res_low>22.60</PDBx:d_res_low>
<PDBx:reflns_acentric>5365</PDBx:reflns_acentric>
<PDBx:reflns_centric>469</PDBx:reflns_centric>
</PDBx:pdbx_phasing_MAD_set>
<PDBx:pdbx_phasing_MAD_set id="ISO_3">
<PDBx:R_cullis_acentric>0.658</PDBx:R_cullis_acentric>
<PDBx:R_cullis_centric>0.500</PDBx:R_cullis_centric>
<PDBx:d_res_high>2.00</PDBx:d_res_high>
<PDBx:d_res_low>22.60</PDBx:d_res_low>
<PDBx:reflns_acentric>5317</PDBx:reflns_acentric>
<PDBx:reflns_centric>460</PDBx:reflns_centric>
</PDBx:pdbx_phasing_MAD_set>
<PDBx:pdbx_phasing_MAD_set id="ANO_1">
<PDBx:R_cullis_acentric>0.841</PDBx:R_cullis_acentric>
<PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric>
<PDBx:d_res_high>2.00</PDBx:d_res_high>
<PDBx:d_res_low>22.60</PDBx:d_res_low>
<PDBx:reflns_acentric>5278</PDBx:reflns_acentric>
<PDBx:reflns_centric>0</PDBx:reflns_centric>
</PDBx:pdbx_phasing_MAD_set>
<PDBx:pdbx_phasing_MAD_set id="ANO_2">
<PDBx:R_cullis_acentric>0.649</PDBx:R_cullis_acentric>
<PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric>
<PDBx:d_res_high>2.00</PDBx:d_res_high>
<PDBx:d_res_low>22.60</PDBx:d_res_low>
<PDBx:reflns_acentric>5083</PDBx:reflns_acentric>
<PDBx:reflns_centric>0</PDBx:reflns_centric>
</PDBx:pdbx_phasing_MAD_set>
<PDBx:pdbx_phasing_MAD_set id="ANO_3">
<PDBx:R_cullis_acentric>0.829</PDBx:R_cullis_acentric>
<PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric>
<PDBx:d_res_high>2.00</PDBx:d_res_high>
<PDBx:d_res_low>22.60</PDBx:d_res_low>
<PDBx:reflns_acentric>5329</PDBx:reflns_acentric>
<PDBx:reflns_centric>0</PDBx:reflns_centric>
</PDBx:pdbx_phasing_MAD_set>
</PDBx:pdbx_phasing_MAD_setCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
pdbx_phasing_MAD_setCategory
This property indicates that datablock
has a category element pdbx_phasing_MAD_set.
pdbx_phasing_MAD_setItem
Abstract Datatype property for pdbx_phasing_MAD_set items.
reference_to_pdbx_phasing_MAD_set
cross-reference to pdbx_phasing_MAD_set
pdbx_phasing_MAD_set.R_cullis
attribute R_cullis in category pdbx_phasing_MAD_set records R_cullis
for MAD phasing.
pdbx_phasing_MAD_set.R_cullis_acentric
attribute R_cullis_acentric in category pdbx_phasing_MAD_set records R_cullis
using acentric data for MAD phasing.
pdbx_phasing_MAD_set.R_cullis_centric
attribute R_cullis_centric in category pdbx_phasing_MAD_set records R_cullis
using centric data for MAD phasing.
pdbx_phasing_MAD_set.R_kraut
attribute R_kraut in category pdbx_phasing_MAD_set records R_kraut
for MAD phasing.
pdbx_phasing_MAD_set.R_kraut_acentric
attribute r_kraut_acentric in category pdbx_phasing_MAD_set records r_kraut
using acentric data for MAD phasing.
pdbx_phasing_MAD_set.R_kraut_centric
attribute R_kraut_centric in category pdbx_phasing_MAD_set records r_kraut
using centric data for MAD phasing.
pdbx_phasing_MAD_set.d_res_high
attribute d_res_high in category pdbx_phasing_MAD_set records the highest resolution
for the phasing set.
pdbx_phasing_MAD_set.d_res_low
attribute d_res_low in category pdbx_phasing_MAD_set records the lowerest
resolution for phasing set.
pdbx_phasing_MAD_set.fom
attribute fom in category pdbx_phasing_MAD_set records the figure of merit
for MAD phasing.
pdbx_phasing_MAD_set.fom_acentric
attribute fom_acentric in category pdbx_phasing_MAD_set records the figure of merit
using acentric data for MAD phasing.
pdbx_phasing_MAD_set.fom_centric
attribute fom_centric in category pdbx_phasing_MAD_set records the figure of merit
using centric data for MAD phasing.
pdbx_phasing_MAD_set.loc
attribute loc in category pdbx_phasing_MAD_set records lack of closure
for MAD phasing.
pdbx_phasing_MAD_set.loc_acentric
attribute loc_acentric in category pdbx_phasing_MAD_set records lack of closure
using acentric data for MAD phasing.
pdbx_phasing_MAD_set.loc_centric
attribute loc_centric in category pdbx_phasing_MAD_set records lack of closure
using centric data for MAD phasing.
pdbx_phasing_MAD_set.number_of_sites
attribute number_of_sites in category pdbx_phasing_MAD_set records the number of site
refined for the phasing set.
pdbx_phasing_MAD_set.power
attribute power in category pdbx_phasing_MAD_set records phasing power
for MAD phasing.
pdbx_phasing_MAD_set.power_acentric
attribute power_acentric in category pdbx_phasing_MAD_set records phasing powe
using acentric data for MAD phasing.
pdbx_phasing_MAD_set.power_centric
attribute power_centric in category pdbx_phasing_MAD_set records phasing powe
using centric data for MAD phasing.
pdbx_phasing_MAD_set.reflns
attribute reflns in category pdbx_phasing_MAD_set records the number of
reflections used for MAD phasing.
pdbx_phasing_MAD_set.reflns_acentric
attribute reflns_acentric in category pdbx_phasing_MAD_set records the number of
acentric reflections for MAD phasing.
pdbx_phasing_MAD_set.reflns_centric
attribute reflns_centric in category pdbx_phasing_MAD_set records the number of
centric reflections for MAD phasing.
pdbx_phasing_MAD_set.id
attribute id in category pdbx_phasing_MAD_set records phase set name
for MAD phasing.
pdbx_phasing_MAD_set_shell
The same as category pdbx_phasing_MAD_set, but
broken into shells.
Example 1 - three wavelengths (SHARP example)
<PDBx:pdbx_phasing_MAD_set_shellCategory>
<PDBx:pdbx_phasing_MAD_set_shell d_res_high="7.77" d_res_low="22.60" id="ISO_1">
<PDBx:R_cullis_acentric>0.000</PDBx:R_cullis_acentric>
<PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric>
<PDBx:power_acentric>0.000</PDBx:power_acentric>
<PDBx:power_centric>0.000</PDBx:power_centric>
<PDBx:reflns_acentric>64</PDBx:reflns_acentric>
<PDBx:reflns_centric>23</PDBx:reflns_centric>
</PDBx:pdbx_phasing_MAD_set_shell>
<PDBx:pdbx_phasing_MAD_set_shell d_res_high="5.67" d_res_low="7.77" id="ISO_1">
<PDBx:R_cullis_acentric>0.000</PDBx:R_cullis_acentric>
<PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric>
<PDBx:power_acentric>0.000</PDBx:power_acentric>
<PDBx:power_centric>0.000</PDBx:power_centric>
<PDBx:reflns_acentric>130</PDBx:reflns_acentric>
<PDBx:reflns_centric>32</PDBx:reflns_centric>
</PDBx:pdbx_phasing_MAD_set_shell>
<PDBx:pdbx_phasing_MAD_set_shell d_res_high="4.68" d_res_low="5.67" id="ISO_1">
<PDBx:R_cullis_acentric>0.000</PDBx:R_cullis_acentric>
<PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric>
<PDBx:power_acentric>0.000</PDBx:power_acentric>
<PDBx:power_centric>0.000</PDBx:power_centric>
<PDBx:reflns_acentric>182</PDBx:reflns_acentric>
<PDBx:reflns_centric>27</PDBx:reflns_centric>
</PDBx:pdbx_phasing_MAD_set_shell>
<PDBx:pdbx_phasing_MAD_set_shell d_res_high="4.07" d_res_low="4.68" id="ISO_1">
<PDBx:R_cullis_acentric>0.000</PDBx:R_cullis_acentric>
<PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric>
<PDBx:power_acentric>0.000</PDBx:power_acentric>
<PDBx:power_centric>0.000</PDBx:power_centric>
<PDBx:reflns_acentric>207</PDBx:reflns_acentric>
<PDBx:reflns_centric>24</PDBx:reflns_centric>
</PDBx:pdbx_phasing_MAD_set_shell>
<PDBx:pdbx_phasing_MAD_set_shell d_res_high="7.77" d_res_low="22.60" id="ANO_1">
<PDBx:R_cullis_acentric>0.610</PDBx:R_cullis_acentric>
<PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric>
<PDBx:power_acentric>1.804</PDBx:power_acentric>
<PDBx:power_centric>0.000</PDBx:power_centric>
<PDBx:reflns_acentric>62</PDBx:reflns_acentric>
<PDBx:reflns_centric>0</PDBx:reflns_centric>
</PDBx:pdbx_phasing_MAD_set_shell>
<PDBx:pdbx_phasing_MAD_set_shell d_res_high="5.67" d_res_low="7.77" id="ANO_1">
<PDBx:R_cullis_acentric>0.532</PDBx:R_cullis_acentric>
<PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric>
<PDBx:power_acentric>2.382</PDBx:power_acentric>
<PDBx:power_centric>0.000</PDBx:power_centric>
<PDBx:reflns_acentric>129</PDBx:reflns_acentric>
<PDBx:reflns_centric>0</PDBx:reflns_centric>
</PDBx:pdbx_phasing_MAD_set_shell>
<PDBx:pdbx_phasing_MAD_set_shell d_res_high="4.68" d_res_low="5.67" id="ANO_1">
<PDBx:R_cullis_acentric>0.673</PDBx:R_cullis_acentric>
<PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric>
<PDBx:power_acentric>1.858</PDBx:power_acentric>
<PDBx:power_centric>0.000</PDBx:power_centric>
<PDBx:reflns_acentric>178</PDBx:reflns_acentric>
<PDBx:reflns_centric>0</PDBx:reflns_centric>
</PDBx:pdbx_phasing_MAD_set_shell>
<PDBx:pdbx_phasing_MAD_set_shell d_res_high="4.07" d_res_low="4.68" id="ANO_1">
<PDBx:R_cullis_acentric>0.755</PDBx:R_cullis_acentric>
<PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric>
<PDBx:power_acentric>1.605</PDBx:power_acentric>
<PDBx:power_centric>0.000</PDBx:power_centric>
<PDBx:reflns_acentric>204</PDBx:reflns_acentric>
<PDBx:reflns_centric>0</PDBx:reflns_centric>
</PDBx:pdbx_phasing_MAD_set_shell>
</PDBx:pdbx_phasing_MAD_set_shellCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
pdbx_phasing_MAD_set_shellCategory
This property indicates that datablock
has a category element pdbx_phasing_MAD_set_shell.
pdbx_phasing_MAD_set_shellItem
Abstract Datatype property for pdbx_phasing_MAD_set_shell items.
reference_to_pdbx_phasing_MAD_set_shell
cross-reference to pdbx_phasing_MAD_set_shell
pdbx_phasing_MAD_set_shell.R_cullis
attribute R_cullis in category pdbx_phasing_MAD_set_shell records R_cullis
for MAD phasing.
pdbx_phasing_MAD_set_shell.R_cullis_acentric
attribute R_cullis_acentric in category pdbx_phasing_MAD_set_shell records R_cullis
using acentric data for MAD phasing.
pdbx_phasing_MAD_set_shell.R_cullis_centric
attribute R_cullis_centric in category pdbx_phasing_MAD_set_shell records R_cullis
using centric data for MAD phasing.
pdbx_phasing_MAD_set_shell.R_kraut
attribute R_kraut in category pdbx_phasing_MAD_set_shell records R_kraut
for MAD phasing.
pdbx_phasing_MAD_set_shell.R_kraut_acentric
attribute R_kraut_acentric in category pdbx_phasing_MAD_set_shell records R_kraut
using acentric data for MAD phasing.
pdbx_phasing_MAD_set_shell.R_kraut_centric
attribute R_kraut_centric in category pdbx_phasing_MAD_set_shell records R_kraut
using centric data for MAD phasing.
pdbx_phasing_MAD_set_shell.fom
attribute fom in category pdbx_phasing_MAD_set_shell records the figure of merit
for MAD phasing.
pdbx_phasing_MAD_set_shell.fom_acentric
attribute fom_acentric in category pdbx_phasing_MAD_set_shell records the figure of merit
using acentric data for MAD phasing.
pdbx_phasing_MAD_set_shell.fom_centric
attribute fom_centric in category pdbx_phasing_MAD_set_shell records the figure of merit
using centric data for MAD phasing.
pdbx_phasing_MAD_set_shell.loc
attribute loc in category pdbx_phasing_MAD_set_shell records lack of closure
for MAD phasing.
pdbx_phasing_MAD_set_shell.loc_acentric
attribute loc_acentric in category pdbx_phasing_MAD_set_shell records lack of closure
using acentric data for MAD phasing.
pdbx_phasing_MAD_set_shell.loc_centric
attribute loc_centric in category pdbx_phasing_MAD_set_shell records lack of closure
using centric data for MAD phasing.
pdbx_phasing_MAD_set_shell.power
attribute power in category pdbx_phasing_MAD_set_shell records phasing power
for MAD phasing.
pdbx_phasing_MAD_set_shell.power_acentric
attribute power_acentric in category pdbx_phasing_MAD_set_shell records phasing power
using acentric data for MAD phasing.
pdbx_phasing_MAD_set_shell.power_centric
attribute power_centric in category pdbx_phasing_MAD_set_shell records phasing power
using centric data for MAD phasing.
pdbx_phasing_MAD_set_shell.reflns
attribute reflns in category pdbx_phasing_MAD_set_shell records the number of
reflections used for MAD phasing.
pdbx_phasing_MAD_set_shell.reflns_acentric
attribute reflns_acentric in category pdbx_phasing_MAD_set_shell records the number of
acentric reflections for MAD phasing.
pdbx_phasing_MAD_set_shell.reflns_centric
attribute reflns_centric in category pdbx_phasing_MAD_set_shell records the number of
centric reflections for MAD phasing.
pdbx_phasing_MAD_set_shell.d_res_high
attribute d_res_high in category pdbx_phasing_MAD_set_shell records the highest resolution
for the phasing set.
pdbx_phasing_MAD_set_shell.d_res_low
attribute d_res_low in category pdbx_phasing_MAD_set_shell records the lowerest
resolution for phasing set.
pdbx_phasing_MAD_set_shell.id
attribute id in category pdbx_phasing_MAD_set_shell records phase set name
for MAD phasing.
pdbx_phasing_MAD_set_site
record the details (coordinates etc.) of anomalous scatters.
Example 1 - anomalous scatters is Se
<PDBx:pdbx_phasing_MAD_set_siteCategory>
<PDBx:pdbx_phasing_MAD_set_site id="1">
<PDBx:Cartn_x>25.9407</PDBx:Cartn_x>
<PDBx:Cartn_y>-0.103471</PDBx:Cartn_y>
<PDBx:Cartn_z>17.4094</PDBx:Cartn_z>
<PDBx:atom_type_symbol>SE</PDBx:atom_type_symbol>
<PDBx:b_iso>15.2561</PDBx:b_iso>
<PDBx:occupancy>1</PDBx:occupancy>
</PDBx:pdbx_phasing_MAD_set_site>
<PDBx:pdbx_phasing_MAD_set_site id="2">
<PDBx:Cartn_x>30.6534</PDBx:Cartn_x>
<PDBx:Cartn_y>6.62359</PDBx:Cartn_y>
<PDBx:Cartn_z>9.93063</PDBx:Cartn_z>
<PDBx:atom_type_symbol>SE</PDBx:atom_type_symbol>
<PDBx:b_iso>12.9102</PDBx:b_iso>
<PDBx:occupancy>1</PDBx:occupancy>
</PDBx:pdbx_phasing_MAD_set_site>
<PDBx:pdbx_phasing_MAD_set_site id="3">
<PDBx:Cartn_x>-3.26506</PDBx:Cartn_x>
<PDBx:Cartn_y>15.5546</PDBx:Cartn_y>
<PDBx:Cartn_z>53.9529</PDBx:Cartn_z>
<PDBx:atom_type_symbol>SE</PDBx:atom_type_symbol>
<PDBx:b_iso>30.5239</PDBx:b_iso>
<PDBx:occupancy>1</PDBx:occupancy>
</PDBx:pdbx_phasing_MAD_set_site>
</PDBx:pdbx_phasing_MAD_set_siteCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
pdbx_phasing_MAD_set_siteCategory
This property indicates that datablock
has a category element pdbx_phasing_MAD_set_site.
pdbx_phasing_MAD_set_siteItem
Abstract Datatype property for pdbx_phasing_MAD_set_site items.
reference_to_pdbx_phasing_MAD_set_site
cross-reference to pdbx_phasing_MAD_set_site
pdbx_phasing_MAD_set_site.Cartn_x
attribute Cartn_x in category pdbx_phasing_MAD_set_site records the X Cartesian
coordinate of site obtained from MAD phasing.
pdbx_phasing_MAD_set_site.Cartn_x_esd
attribute Cartn_x_esd in category pdbx_phasing_MAD_set_site records the estimated
standard deviation X Cartesian
coordinate of site obtained from MAD phasing.
pdbx_phasing_MAD_set_site.Cartn_y
attribute Cartn_y in category pdbx_phasing_MAD_set_site records the Y Cartesian
coordinate of site obtained from MAD phasing.
pdbx_phasing_MAD_set_site.Cartn_y_esd
attribute Cartn_y_esd in category pdbx_phasing_MAD_set_site records the estimated
standard deviation Y Cartesian
coordinate of site obtained from MAD phasing.
pdbx_phasing_MAD_set_site.Cartn_z
attribute Cartn_z in category pdbx_phasing_MAD_set_site records the Z Cartesian
coordinate of site obtained from MAD phasing.
pdbx_phasing_MAD_set_site.Cartn_z_esd
attribute Cartn_z_esd in category pdbx_phasing_MAD_set_site records the estimated
standard deviation Z Cartesian
coordinate of site obtained from MAD phasing.
pdbx_phasing_MAD_set_site.atom_type_symbol
attribute atom_type_symbol in category pdbx_phasing_MAD_set_site records the name of site
obtained from MAD phasing.
pdbx_phasing_MAD_set_site.b_iso
attribute b_iso in category pdbx_phasing_MAD_set_site records isotropic
temperature factor parameterthe for the site
obtained from MAD phasing.
pdbx_phasing_MAD_set_site.b_iso_esd
attribute b_iso_esd in category pdbx_phasing_MAD_set_site records estimated
standard deviation of isotropic
temperature factor parameterthe for the site
obtained from MAD phasing.
pdbx_phasing_MAD_set_site.fract_x
attribute fract_x in category pdbx_phasing_MAD_set_site records the X fractional
coordinate of site obtained from MAD phasing.
pdbx_phasing_MAD_set_site.fract_x_esd
attribute fract_x_esd in category pdbx_phasing_MAD_set_site records the estimated
standard deviation X fractional
coordinate of site obtained from MAD phasing.
pdbx_phasing_MAD_set_site.fract_y
attribute fract_y in category pdbx_phasing_MAD_set_site records the Y fractional
coordinate of site obtained from MAD phasing.
pdbx_phasing_MAD_set_site.fract_y_esd
attribute fract_y_esd in category pdbx_phasing_MAD_set_site records the estimated
standard deviation Y fractional
coordinate of site obtained from MAD phasing.
pdbx_phasing_MAD_set_site.fract_z
attribute fract_z in category pdbx_phasing_MAD_set_site records the Z fractional
coordinate of site obtained from MAD phasing.
pdbx_phasing_MAD_set_site.fract_z_esd
attribute fract_z_esd in category pdbx_phasing_MAD_set_site records the estimated
standard deviation Z fractional
coordinate of site obtained from MAD phasing.
pdbx_phasing_MAD_set_site.occupancy
attribute occupancy in category pdbx_phasing_MAD_set_site records the fraction
of the atom type presented at this site.
pdbx_phasing_MAD_set_site.occupancy_esd
attribute occupancy_esd in category pdbx_phasing_MAD_set_site records estimated
standard deviation of the fraction
of the atom type presented at this site.
pdbx_phasing_MAD_set_site.occupancy_iso
The relative real isotropic occupancy of the atom type
present at this heavy-atom site in a given atom site.
pdbx_phasing_MAD_set_site.set_id
record the phasing set.
pdbx_phasing_MAD_set_site.id
attribute id in category pdbx_phasing_MAD_set_site records the number of site
obtained from MAD phasing.
pdbx_phasing_MAD_shell
Data items in the PDBX_PHASING_MAD_SHELL category record details about
the phasing of the structure, when methods involving multiple
anomalous dispersion techniques are involved (note: the
values are overall, but broken down into shells of resolution)
Example 1 -
<PDBx:pdbx_phasing_MAD_shellCategory>
<PDBx:pdbx_phasing_MAD_shell d_res_high="7.77" d_res_low="22.60">
<PDBx:fom_acentric>0.886</PDBx:fom_acentric>
<PDBx:fom_centric>0.641</PDBx:fom_centric>
<PDBx:reflns_acentric>64</PDBx:reflns_acentric>
<PDBx:reflns_centric>23</PDBx:reflns_centric>
</PDBx:pdbx_phasing_MAD_shell>
<PDBx:pdbx_phasing_MAD_shell d_res_high="5.67" d_res_low="7.77">
<PDBx:fom_acentric>0.863</PDBx:fom_acentric>
<PDBx:fom_centric>0.642</PDBx:fom_centric>
<PDBx:reflns_acentric>132</PDBx:reflns_acentric>
<PDBx:reflns_centric>32</PDBx:reflns_centric>
</PDBx:pdbx_phasing_MAD_shell>
<PDBx:pdbx_phasing_MAD_shell d_res_high="4.68" d_res_low="5.67">
<PDBx:fom_acentric>0.842</PDBx:fom_acentric>
<PDBx:fom_centric>0.737</PDBx:fom_centric>
<PDBx:reflns_acentric>182</PDBx:reflns_acentric>
<PDBx:reflns_centric>27</PDBx:reflns_centric>
</PDBx:pdbx_phasing_MAD_shell>
<PDBx:pdbx_phasing_MAD_shell d_res_high="4.07" d_res_low="4.68">
<PDBx:fom_acentric>0.789</PDBx:fom_acentric>
<PDBx:fom_centric>0.682</PDBx:fom_centric>
<PDBx:reflns_acentric>209</PDBx:reflns_acentric>
<PDBx:reflns_centric>24</PDBx:reflns_centric>
</PDBx:pdbx_phasing_MAD_shell>
<PDBx:pdbx_phasing_MAD_shell d_res_high="3.65" d_res_low="4.07">
<PDBx:fom_acentric>0.772</PDBx:fom_acentric>
<PDBx:fom_centric>0.633</PDBx:fom_centric>
<PDBx:reflns_acentric>246</PDBx:reflns_acentric>
<PDBx:reflns_centric>27</PDBx:reflns_centric>
</PDBx:pdbx_phasing_MAD_shell>
<PDBx:pdbx_phasing_MAD_shell d_res_high="3.34" d_res_low="3.65">
<PDBx:fom_acentric>0.752</PDBx:fom_acentric>
<PDBx:fom_centric>0.700</PDBx:fom_centric>
<PDBx:reflns_acentric>260</PDBx:reflns_acentric>
<PDBx:reflns_centric>31</PDBx:reflns_centric>
</PDBx:pdbx_phasing_MAD_shell>
</PDBx:pdbx_phasing_MAD_shellCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
pdbx_phasing_MAD_shellCategory
This property indicates that datablock
has a category element pdbx_phasing_MAD_shell.
pdbx_phasing_MAD_shellItem
Abstract Datatype property for pdbx_phasing_MAD_shell items.
reference_to_pdbx_phasing_MAD_shell
cross-reference to pdbx_phasing_MAD_shell
pdbx_phasing_MAD_shell.R_cullis
attribute R_cullis in category pdbx_phasing_MAD_shell records R_cullis
for MAD phasing.
pdbx_phasing_MAD_shell.R_cullis_acentric
attribute R_cullis_acentric in category pdbx_phasing_MAD_shell records R_cullis
using acentric data for MAD phasing.
pdbx_phasing_MAD_shell.R_cullis_centric
attribute R_cullis_centric in category pdbx_phasing_MAD_shell records R_cullis
using centric data for MAD phasing.
pdbx_phasing_MAD_shell.R_kraut
attribute R_kraut in category pdbx_phasing_MAD_shell records R_kraut
for MAD phasing.
pdbx_phasing_MAD_shell.R_kraut_acentric
attribute r_kraut_acentric in category pdbx_phasing_MAD_shell records R_kraut
using acentric data for MAD phasing.
pdbx_phasing_MAD_shell.R_kraut_centric
attribute R_kraut_centric in category pdbx_phasing_MAD_shell records R_kraut
using centric data for MAD phasing.
pdbx_phasing_MAD_shell.fom
attribute fom in category pdbx_phasing_MAD_shell records the figure of merit
for MAD phasing.
pdbx_phasing_MAD_shell.fom_acentric
attribute fom_acentric in category pdbx_phasing_MAD_shell records the figure of merit
using acentric data for MAD phasing.
pdbx_phasing_MAD_shell.fom_centric
attribute fom_centric in category pdbx_phasing_MAD_shell records the figure of merit
using centric data for MAD phasing.
pdbx_phasing_MAD_shell.loc
attribute loc in category pdbx_phasing_MAD_shell records lack of closure
for MAD phasing.
pdbx_phasing_MAD_shell.loc_acentric
attribute loc_acentric in category pdbx_phasing_MAD_shell records lack of closure
using acentric data for MAD phasing.
pdbx_phasing_MAD_shell.loc_centric
attribute loc_centric in category pdbx_phasing_MAD_shell records lack of closure
using centric data for MAD phasing.
pdbx_phasing_MAD_shell.power
attribute loc in category pdbx_phasing_MAD_shell records phasing power
for MAD phasing.
pdbx_phasing_MAD_shell.power_acentric
attribute power_acentric in category pdbx_phasing_MAD_shell records phasing powe
using acentric data for MAD phasing.
pdbx_phasing_MAD_shell.power_centric
attribute power_centric in category pdbx_phasing_MAD_shell records phasing powe
using centric data for MAD phasing.
pdbx_phasing_MAD_shell.reflns
attribute reflns in category pdbx_phasing_MAD_shell records the number of
reflections used for MAD phasing.
pdbx_phasing_MAD_shell.reflns_acentric
attribute reflns_acentric in category pdbx_phasing_MAD_shell records the number of
acentric reflections for MAD phasing.
pdbx_phasing_MAD_shell.reflns_centric
attribute reflns_centric in category pdbx_phasing_MAD_shell records the number of
centric reflections for MAD phasing.
pdbx_phasing_MAD_shell.d_res_high
attribute d_res_high in category pdbx_phasing_MAD_shell records the higher resolution
for the shell.
pdbx_phasing_MAD_shell.d_res_low
attribute d_res_low in category pdbx_phasing_MAD_shell records the lower resolution
for the shell.
pdbx_phasing_MR
Data items in the PDBX_PHASING_MR category record details about
molecular replacement.
Example 1 - molecular replacement example from program CNS.
<PDBx:pdbx_phasing_MRCategory>
<PDBx:pdbx_phasing_MR entry_id="ABC001">
<PDBx:correlation_coeff_Fo_to_Fc>0.586</PDBx:correlation_coeff_Fo_to_Fc>
<PDBx:d_res_high_rotation>3.8</PDBx:d_res_high_rotation>
<PDBx:d_res_high_translation>4.0</PDBx:d_res_high_translation>
<PDBx:d_res_low_rotation>13.0</PDBx:d_res_low_rotation>
<PDBx:d_res_low_translation>15.0</PDBx:d_res_low_translation>
<PDBx:method_rotation>real-space rotation search</PDBx:method_rotation>
<PDBx:method_translation>gerneral using PC-refinement= e2e2</PDBx:method_translation>
<PDBx:packing>0.3086</PDBx:packing>
<PDBx:reflns_percent_rotation>97.8</PDBx:reflns_percent_rotation>
<PDBx:reflns_percent_translation>97.7</PDBx:reflns_percent_translation>
<PDBx:sigma_F_rotation>1.0</PDBx:sigma_F_rotation>
<PDBx:sigma_F_translation>0</PDBx:sigma_F_translation>
</PDBx:pdbx_phasing_MR>
</PDBx:pdbx_phasing_MRCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
pdbx_phasing_MRCategory
This property indicates that datablock
has a category element pdbx_phasing_MR.
pdbx_phasing_MRItem
Abstract Datatype property for pdbx_phasing_MR items.
reference_to_pdbx_phasing_MR
cross-reference to pdbx_phasing_MR
pdbx_phasing_MR.R_factor
The value of attribute R_factor in category pdbx_phasing_MR identifies the R factor
(defined as uasual) after rotation and translation.
pdbx_phasing_MR.R_rigid_body
The value of attribute R_rigid_body in category pdbx_phasing_MR identifies the R factor
for rigid body refinement after rotation and translation.(In general,
rigid body refinement has to be carried out after molecular
replacement.
pdbx_phasing_MR.correlation_coeff_Fo_to_Fc
The value of attribute correlation_coeff_Fo_to_Fc in category pdbx_phasing_MR identifies
the correlation between the observed and the calculated structure
factor after rotation and translation.
pdbx_phasing_MR.correlation_coeff_Io_to_Ic
The value of attribute correlation_coeff_Io_to_Ic in category pdbx_phasing_MR identifies
the correlation between the observed and the calculated intensity
(~|F|^2) after rotation and translation.
pdbx_phasing_MR.d_res_high_rotation
The value of attribute d_res_high_rotation in category pdbx_phasing_MR identifies
the highest resolution used for rotation search.
pdbx_phasing_MR.d_res_high_translation
The value of attribute d_res_high_translation in category pdbx_phasing_MR identifies
the highest resolution used for translation search.
pdbx_phasing_MR.d_res_low_rotation
The value of attribute d_res_low_rotation in category pdbx_phasing_MR identifies
the lowest resolution used for rotation search.
pdbx_phasing_MR.d_res_low_translation
The value of attribute d_res_low_translation in category pdbx_phasing_MR identifies
the lowest resolution used for translation search.
pdbx_phasing_MR.method_rotation
The value of attribute method_rotation in category pdbx_phasing_MR identifies the method
used for rotation search. For example, the rotation method may be
realspace, fastdirect, or direct.
.
pdbx_phasing_MR.method_translation
The value of attribute method_translation in category pdbx_phasing_MR identifies the method
used for translation search. For example in CNS, the translation method
may be "general" or "phased" with PC refinement target using
"fastf2f2" "e2e2" "e1e1" "f2f2" "f1f1" "residual" "vector".
.
pdbx_phasing_MR.model_details
The value of attribute model_details in category pdbx_phasing_MR records the details of
model used. For example, the original model can be truncated by
deleting side chains, doubtful parts, using the monomer if the
original model was an oligomer. The search model may be one
domain of a large molecule. What is the pdb IDs.
pdbx_phasing_MR.native_set_id
The data set that was treated as the native in this
experiment.
This data item is a pointer to attribute id in category phasing_set in the
PHASING_SET category.
pdbx_phasing_MR.packing
The value of attribute packing in category pdbx_phasing_MR identifies the packing of
search model in the unit cell. Too many crystallographic contacts
may indicate a bad search.
pdbx_phasing_MR.reflns_percent_rotation
The value of attribute reflns_percent_rotation in category pdbx_phasing_MR identifies the
completness of data used for rotation search.
pdbx_phasing_MR.reflns_percent_translation
The value of attribute reflns_percent_translation in category pdbx_phasing_MR identifies the
completness of data used for translation search.
pdbx_phasing_MR.sigma_F_rotation
The value of attribute sigma_F_rotation in category pdbx_phasing_MR identifies the
sigma cut off of structure factor used for rotation search.
pdbx_phasing_MR.sigma_F_translation
The value of attribute sigma_F_translation in category pdbx_phasing_MR identifies the
sigma cut off of structure factor used for translation search.
pdbx_phasing_MR.sigma_I_rotation
The value of attribute sigma_I_rotation in category pdbx_phasing_MR identifies the
sigma cut off of intensity used for rotation search.
pdbx_phasing_MR.sigma_I_translation
The value of attribute sigma_I_translation in category pdbx_phasing_MR identifies the
sigma cut off of intensity used for translation search.
pdbx_phasing_MR.entry_id
The value of attribute entry_id in category pdbx_phasing_MR identifies the data block.
pdbx_phasing_dm
Data items in the PDBX_PHASING_DM category record details about
density modification
Example 1 - density modification from resolve
<PDBx:pdbx_phasing_dmCategory>
<PDBx:pdbx_phasing_dm entry_id="ABC001">
<PDBx:fom>0.85</PDBx:fom>
<PDBx:fom_acentric>0.85</PDBx:fom_acentric>
<PDBx:fom_centric>0.79</PDBx:fom_centric>
<PDBx:reflns>12486</PDBx:reflns>
<PDBx:reflns_acentric>11351</PDBx:reflns_acentric>
<PDBx:reflns_centric>1135</PDBx:reflns_centric>
</PDBx:pdbx_phasing_dm>
</PDBx:pdbx_phasing_dmCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
pdbx_phasing_dmCategory
This property indicates that datablock
has a category element pdbx_phasing_dm.
pdbx_phasing_dmItem
Abstract Datatype property for pdbx_phasing_dm items.
reference_to_pdbx_phasing_dm
cross-reference to pdbx_phasing_dm
pdbx_phasing_dm.delta_phi_final
The value of attribute delta_phi_final in category pdbx_phasing_dm identifies phase difference
after density modification
pdbx_phasing_dm.delta_phi_initial
The value of attribute delta_phi_initial in category pdbx_phasing_dm identifies phase difference
before density modification
pdbx_phasing_dm.fom
The value of attribute fom in category pdbx_phasing_dm identifies the figure of merit
for all the data
pdbx_phasing_dm.fom_acentric
The value of attribute fom_acentric in category pdbx_phasing_dm identifies the figure of merit
for acentric data
pdbx_phasing_dm.fom_centric
The value of attribute fom_centric in category pdbx_phasing_dm identifies the figure of merit
for acentric data
pdbx_phasing_dm.mask_type
The value of attribute mask_type in category pdbx_phasing_dm identifies the type of mask used for
density modification
pdbx_phasing_dm.method
The value of attribute method in category pdbx_phasing_dm identifies the method used for
density modification
pdbx_phasing_dm.reflns
The value of attribute reflns in category pdbx_phasing_dm identifies the number
of centric and acentric reflections.
pdbx_phasing_dm.reflns_acentric
The value of attribute reflns_acentric in category pdbx_phasing_dm identifies the number
of acentric reflections.
pdbx_phasing_dm.reflns_centric
The value of attribute reflns_centric in category pdbx_phasing_dm identifies the number
of centric reflections.
pdbx_phasing_dm.entry_id
The value of attribute entry_id in category pdbx_phasing_dm identifies the data block.
pdbx_phasing_dm_shell
Data items in the PDBX_PHASING_DM_SHELL category record details about
density modification in resolution shell.
Example 1 - density modification with shells
<PDBx:pdbx_phasing_dm_shellCategory>
<PDBx:pdbx_phasing_dm_shell d_res_high="7.73" d_res_low="100.00">
<PDBx:delta_phi_final>24.7</PDBx:delta_phi_final>
<PDBx:fom>0.879</PDBx:fom>
<PDBx:reflns>502</PDBx:reflns>
</PDBx:pdbx_phasing_dm_shell>
<PDBx:pdbx_phasing_dm_shell d_res_high="6.24" d_res_low="7.73">
<PDBx:delta_phi_final>29.2</PDBx:delta_phi_final>
<PDBx:fom>0.857</PDBx:fom>
<PDBx:reflns>506</PDBx:reflns>
</PDBx:pdbx_phasing_dm_shell>
<PDBx:pdbx_phasing_dm_shell d_res_high="5.50" d_res_low="6.24">
<PDBx:delta_phi_final>29.2</PDBx:delta_phi_final>
<PDBx:fom>0.838</PDBx:fom>
<PDBx:reflns>504</PDBx:reflns>
</PDBx:pdbx_phasing_dm_shell>
<PDBx:pdbx_phasing_dm_shell d_res_high="5.02" d_res_low="5.50">
<PDBx:delta_phi_final>25.3</PDBx:delta_phi_final>
<PDBx:fom>0.851</PDBx:fom>
<PDBx:reflns>502</PDBx:reflns>
</PDBx:pdbx_phasing_dm_shell>
<PDBx:pdbx_phasing_dm_shell d_res_high="4.67" d_res_low="5.02">
<PDBx:delta_phi_final>22.7</PDBx:delta_phi_final>
<PDBx:fom>0.831</PDBx:fom>
<PDBx:reflns>503</PDBx:reflns>
</PDBx:pdbx_phasing_dm_shell>
</PDBx:pdbx_phasing_dm_shellCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
pdbx_phasing_dm_shellCategory
This property indicates that datablock
has a category element pdbx_phasing_dm_shell.
pdbx_phasing_dm_shellItem
Abstract Datatype property for pdbx_phasing_dm_shell items.
reference_to_pdbx_phasing_dm_shell
cross-reference to pdbx_phasing_dm_shell
pdbx_phasing_dm_shell.delta_phi_final
The value of attribute delta_phi_final in category pdbx_phasing_dm_shell identifies phase difference
after density modification with resolution shells.
pdbx_phasing_dm_shell.delta_phi_initial
The value of attribute delta_phi_initial in category pdbx_phasing_dm_shell identifies phase difference
before density modification with resolution shells.
pdbx_phasing_dm_shell.fom
The value of attribute fom in category pdbx_phasing_dm_shell identifies the figure of merit
for all the data with resolution shells.
pdbx_phasing_dm_shell.fom_acentric
The value of attribute fom_acentric in category pdbx_phasing_dm_shell identifies the figure of merit
for acentric data with resolution shells
pdbx_phasing_dm_shell.fom_centric
The value of attribute fom_centric in category pdbx_phasing_dm_shell identifies the figure of merit
for centric data with resolution shells.
pdbx_phasing_dm_shell.reflns
The value of attribute reflns in category pdbx_phasing_dm_shell identifies the number
of centric and acentric reflections with resolution shells.
pdbx_phasing_dm_shell.reflns_acentric
The value of attribute reflns_acentric in category pdbx_phasing_dm_shell identifies the number
of acentric reflections with resolution shells.
pdbx_phasing_dm_shell.reflns_centric
The value of attribute reflns_centric in category pdbx_phasing_dm_shell identifies the number
of centric reflections with resolution shells.
pdbx_phasing_dm_shell.d_res_high
The value of attribute d_res_high in category pdbx_phasing_dm_shell identifies high resolution
pdbx_phasing_dm_shell.d_res_low
The value of attribute d_res_low in category pdbx_phasing_dm_shell identifies low resolution
pdbx_point_symmetry
Data items in the PDBX_POINT_SYMMETRY category record details about the
point symmetry group associated with this entry.
Example 1 -
<PDBx:pdbx_point_symmetryCategory>
<PDBx:pdbx_point_symmetry entry_id="1ABC">
<PDBx:H-M_notation>532</PDBx:H-M_notation>
<PDBx:Schoenflies_symbol>I</PDBx:Schoenflies_symbol>
</PDBx:pdbx_point_symmetry>
</PDBx:pdbx_point_symmetryCategory>
0
1
1
1
0
1
1
pdbx_point_symmetryCategory
This property indicates that datablock
has a category element pdbx_point_symmetry.
pdbx_point_symmetryItem
Abstract Datatype property for pdbx_point_symmetry items.
reference_to_pdbx_point_symmetry
cross-reference to pdbx_point_symmetry
pdbx_point_symmetry.H-M_notation
The Hermann-Mauguin notation for this point symmetry group.
I -> 532
O -> 432
T -> 23
Cn -> n (e.g. C5 -> 5)
Dn -> n22 (n even)
Dn -> n2 (n odd)
I
O
T
C
D
The Schoenflies point symmetry symbol.
pdbx_point_symmetry.circular_symmetry
Rotational n-fold C and D point symmetry.
pdbx_point_symmetry.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
pdbx_poly_seq_scheme
The PDBX_POLY_SEQ_SCHEME category provides residue level nomenclature
mapping for polymer entities.
Example 1 - based on NDB entry DDFB25
<PDBx:pdbx_poly_seq_schemeCategory>
<PDBx:pdbx_poly_seq_scheme asym_id="A" entity_id="1" mon_id="DC" seq_id="1">
<PDBx:auth_mon_id>DC</PDBx:auth_mon_id>
<PDBx:auth_seq_num>1</PDBx:auth_seq_num>
<PDBx:ndb_seq_num>1</PDBx:ndb_seq_num>
<PDBx:pdb_ins_code></PDBx:pdb_ins_code>
<PDBx:pdb_mon_id>DC</PDBx:pdb_mon_id>
<PDBx:pdb_seq_num>1</PDBx:pdb_seq_num>
<PDBx:pdb_strand_id>A</PDBx:pdb_strand_id>
</PDBx:pdbx_poly_seq_scheme>
<PDBx:pdbx_poly_seq_scheme asym_id="A" entity_id="1" mon_id="DG" seq_id="2">
<PDBx:auth_mon_id>DG</PDBx:auth_mon_id>
<PDBx:auth_seq_num>2</PDBx:auth_seq_num>
<PDBx:ndb_seq_num>2</PDBx:ndb_seq_num>
<PDBx:pdb_ins_code></PDBx:pdb_ins_code>
<PDBx:pdb_mon_id>DG</PDBx:pdb_mon_id>
<PDBx:pdb_seq_num>2</PDBx:pdb_seq_num>
<PDBx:pdb_strand_id>A</PDBx:pdb_strand_id>
</PDBx:pdbx_poly_seq_scheme>
<PDBx:pdbx_poly_seq_scheme asym_id="A" entity_id="1" mon_id="DT" seq_id="3">
<PDBx:auth_mon_id>DT</PDBx:auth_mon_id>
<PDBx:auth_seq_num>3</PDBx:auth_seq_num>
<PDBx:ndb_seq_num>3</PDBx:ndb_seq_num>
<PDBx:pdb_ins_code></PDBx:pdb_ins_code>
<PDBx:pdb_mon_id>DT</PDBx:pdb_mon_id>
<PDBx:pdb_seq_num>3</PDBx:pdb_seq_num>
<PDBx:pdb_strand_id>A</PDBx:pdb_strand_id>
</PDBx:pdbx_poly_seq_scheme>
<PDBx:pdbx_poly_seq_scheme asym_id="A" entity_id="1" mon_id="DA" seq_id="4">
<PDBx:auth_mon_id>DA</PDBx:auth_mon_id>
<PDBx:auth_seq_num>4</PDBx:auth_seq_num>
<PDBx:ndb_seq_num>4</PDBx:ndb_seq_num>
<PDBx:pdb_ins_code></PDBx:pdb_ins_code>
<PDBx:pdb_mon_id>DA</PDBx:pdb_mon_id>
<PDBx:pdb_seq_num>4</PDBx:pdb_seq_num>
<PDBx:pdb_strand_id>A</PDBx:pdb_strand_id>
</PDBx:pdbx_poly_seq_scheme>
<PDBx:pdbx_poly_seq_scheme asym_id="A" entity_id="1" mon_id="DC" seq_id="5">
<PDBx:auth_mon_id>DC</PDBx:auth_mon_id>
<PDBx:auth_seq_num>5</PDBx:auth_seq_num>
<PDBx:ndb_seq_num>5</PDBx:ndb_seq_num>
<PDBx:pdb_ins_code></PDBx:pdb_ins_code>
<PDBx:pdb_mon_id>DC</PDBx:pdb_mon_id>
<PDBx:pdb_seq_num>5</PDBx:pdb_seq_num>
<PDBx:pdb_strand_id>A</PDBx:pdb_strand_id>
</PDBx:pdbx_poly_seq_scheme>
<PDBx:pdbx_poly_seq_scheme asym_id="A" entity_id="1" mon_id="DG" seq_id="6">
<PDBx:auth_mon_id>DG</PDBx:auth_mon_id>
<PDBx:auth_seq_num>6</PDBx:auth_seq_num>
<PDBx:ndb_seq_num>6</PDBx:ndb_seq_num>
<PDBx:pdb_ins_code></PDBx:pdb_ins_code>
<PDBx:pdb_mon_id>DG</PDBx:pdb_mon_id>
<PDBx:pdb_seq_num>6</PDBx:pdb_seq_num>
<PDBx:pdb_strand_id>A</PDBx:pdb_strand_id>
</PDBx:pdbx_poly_seq_scheme>
</PDBx:pdbx_poly_seq_schemeCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
pdbx_poly_seq_schemeCategory
This property indicates that datablock
has a category element pdbx_poly_seq_scheme.
pdbx_poly_seq_schemeItem
Abstract Datatype property for pdbx_poly_seq_scheme items.
reference_to_pdbx_poly_seq_scheme
cross-reference to pdbx_poly_seq_scheme
pdbx_poly_seq_scheme.auth_mon_id
attribute auth_comp_id in category atom_site
pdbx_poly_seq_scheme.auth_seq_num
attribute auth_seq_id in category atom_site
no
n
yes
y
Pointer to attribute hetero in category entity_poly_seq
pdbx_poly_seq_scheme.ndb_seq_num
NDB residue number.
pdbx_poly_seq_scheme.pdb_ins_code
PDB insertion code.
pdbx_poly_seq_scheme.pdb_mon_id
PDB residue name.
pdbx_poly_seq_scheme.pdb_seq_num
PDB residue number.
pdbx_poly_seq_scheme.pdb_strand_id
PDB strand/chain id.
pdbx_poly_seq_scheme.asym_id
Pointer to attribute label_asym_id in category atom_site.
1
A
2B3
pdbx_poly_seq_scheme.entity_id
Pointer to attribute id in category entity.
pdbx_poly_seq_scheme.mon_id
Pointer to attribute mon_id in category entity_poly_seq.
pdbx_poly_seq_scheme.seq_id
Pointer to attribute num in category entity_poly_seq
pdbx_prerelease_seq
This category provides a placeholder for pre-release
sequence information. After release this category
should be discarded.
<PDBx:pdbx_prerelease_seqCategory>
<PDBx:pdbx_prerelease_seq entity_id="1">
<PDBx:seq_one_letter_code>GKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD</PDBx:seq_one_letter_code>
</PDBx:pdbx_prerelease_seq>
<PDBx:pdbx_prerelease_seq entity_id="2">
<PDBx:seq_one_letter_code>HKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNN</PDBx:seq_one_letter_code>
</PDBx:pdbx_prerelease_seq>
</PDBx:pdbx_prerelease_seqCategory>
0
1
1
pdbx_prerelease_seqCategory
This property indicates that datablock
has a category element pdbx_prerelease_seq.
pdbx_prerelease_seqItem
Abstract Datatype property for pdbx_prerelease_seq items.
reference_to_pdbx_prerelease_seq
cross-reference to pdbx_prerelease_seq
pdbx_prerelease_seq.seq_one_letter_code
Chemical sequence expressed as string of one-letter
amino acid codes.
A for alanine or adenine
B for ambiguous asparagine/aspartic-acid
R for arginine
N for asparagine
D for aspartic-acid
C for cysteine or cystine or cytosine
Q for glutamine
E for glutamic-acid
Z for ambiguous glutamine/glutamic acid
G for glycine or guanine
H for histidine
I for isoleucine
L for leucine
K for lysine
M for methionine
F for phenylalanine
P for proline
S for serine
T for threonine or thymine
W for tryptophan
Y for tyrosine
V for valine
U for uracil
MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD
pdbx_prerelease_seq.entity_id
This data item is a pointer to attribute id in category entity in the ENTITY category.
pdbx_re_refinement
Describes the origin of the experimental data used in this
entry.
Example 1 -
<PDBx:pdbx_re_refinementCategory>
<PDBx:pdbx_re_refinement entry_id="1ABC">
<PDBx:citation_id>2</PDBx:citation_id>
<PDBx:details>Re-refinement of data from entry 1ABC</PDBx:details>
</PDBx:pdbx_re_refinement>
</PDBx:pdbx_re_refinementCategory>
1
1
1
1
1
pdbx_re_refinementCategory
This property indicates that datablock
has a category element pdbx_re_refinement.
pdbx_re_refinementItem
Abstract Datatype property for pdbx_re_refinement items.
reference_to_pdbx_re_refinement
cross-reference to pdbx_re_refinement
pdbx_re_refinement.citation_id
A pointer to attribute id in category citation in category CITATION describing the
the citation of the entry from from which the experimental data
was obtained.
pdbx_re_refinement.details
Additional details about this re-refinement.
pdbx_re_refinement.entry_id
The identifier for entry where the experimental data was obtained.
pdbx_reference_entity
Data items in the PDBX_REFERENCE_ENTITY category records
reference information about small polymer molecules.
Example: 1 Thiostrepton
<PDBx:pdbx_reference_entityCategory>
<PDBx:pdbx_reference_entity id="1">
<PDBx:description> Thiostrepton complex bacterial natural product containing thiazole
rings that's used as a topical veterinary antibiotic and also has
promising antimalarial and anticancer activity first isolated from
bacteria in 1955, thiostrepton has an unusual type of antibiotic
activity: It disables protein biosynthesis by binding to ribosomal
RNA and one of its associated proteins and interacts directly with
23S rRNA nucleotides 1067A and 1095A</PDBx:description>
<PDBx:details> Thiostrepton is a macrocyclic antibiotic incorporating thiazoles and
other atypical amino acids. Patented in 1961, thiostrepton has been
used as an antibiotic and acts by binding to ribosomes to prevent the
binding of the EF-G elongation factor and GTP to the 50S riobsomal
subunit. Thiostrepton is an inducer of tipA, a gene that controls the
bacterial transcription regulators, TipAL and TipAS, members of the
MerR proteins that are central regulators in multidrug
resistance. Closely related to siomycin, a recently discovered
inhibitor of oncogenic transcription factor - FoxM1. The
thiostrepton-resistant gene is also commonly used as a selective
marker for recombinant DNA/plasmid technologies.</PDBx:details>
<PDBx:formula>C72 H85 N19 O18 S5</PDBx:formula>
<PDBx:formula_weight>1664.83</PDBx:formula_weight>
<PDBx:name>THIOSTREPTON</PDBx:name>
<PDBx:type>macrolide</PDBx:type>
</PDBx:pdbx_reference_entity>
</PDBx:pdbx_reference_entityCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
pdbx_reference_entityCategory
This property indicates that datablock
has a category element pdbx_reference_entity.
pdbx_reference_entityItem
Abstract Datatype property for pdbx_reference_entity items.
reference_to_pdbx_reference_entity
cross-reference to pdbx_reference_entity
pdbx_reference_entity._3-letter-code
For entities represented as single molecules, the 3-letter-code
corresponding to the chemical definition for the molecule.
0Z3
CD9
pdbx_reference_entity.description
A description of the reference entity.
pdbx_reference_entity.details
A description of special aspects of the entity.
pdbx_reference_entity.formula
The formula for the reference entity. Formulae are written
according to the rules:
1. Only recognised element symbols may be used.
2. Each element symbol is followed by a 'count' number. A count
of '1' may be omitted.
3. A space or parenthesis must separate each element symbol and
its count, but in general parentheses are not used.
4. The order of elements depends on whether or not carbon is
present. If carbon is present, the order should be: C, then
H, then the other elements in alphabetical order of their
symbol. If carbon is not present, the elements are listed
purely in alphabetic order of their symbol. This is the
'Hill' system used by Chemical Abstracts.
C18 H19 N7 O8 S
pdbx_reference_entity.formula_weight
Formula mass in daltons of the entity.
pdbx_reference_entity.name
A name of the entity.
thiostrepton
polymer
single molecule
Defines how this entity is represented in PDB data files.
pdbx_reference_entity.type
Defines the type of the entity.
peptide-like
macrolide
pdbx_reference_entity.id
The value of attribute id in category pdbx_reference_entity must uniquely identify a record in the
PDBX_REFERENCE_ENTITY list.
Note that this item need not be a number; it can be any unique
identifier.
pdbx_reference_entity_annotation
Data items in the PDBX_REFERENCE_ENTITY_ANNOTATION category specify
additional annotation relevant to the molecular entities.
Example 1 -
<PDBx:pdbx_reference_entity_annotationCategory>
<PDBx:pdbx_reference_entity_annotation entity_id="1" text="antigen binding" type="molecular function">
<PDBx:support> Experimentally verified with fluroescent antigen using flow cytometry</PDBx:support>
</PDBx:pdbx_reference_entity_annotation>
</PDBx:pdbx_reference_entity_annotationCategory>
1
1
0
1
1
1
1
pdbx_reference_entity_annotationCategory
This property indicates that datablock
has a category element pdbx_reference_entity_annotation.
pdbx_reference_entity_annotationItem
Abstract Datatype property for pdbx_reference_entity_annotation items.
reference_to_pdbx_reference_entity_annotation
cross-reference to pdbx_reference_entity_annotation
pdbx_reference_entity_annotation.source
The information source for the entity annotation.
Author provided
UniProt
PubChem
pdbx_reference_entity_annotation.support
Text describing the experimentation or computational evidence for
the annotation.
fluoresence measurements using flow cytometry
kinase binding assay
pdbx_reference_entity_annotation.entity_id
This data item is a pointer to attribute id in category pdbx_reference_entity in the
PDB_REFERENCE_ENTITY category.
pdbx_reference_entity_annotation.text
Text describing the annotation for this entity.
antigen binding
glucose transporter activity
pdbx_reference_entity_annotation.type
Type of annoation for this entity.
molecular function
biochemical pathway
biomedical function
other annotation
pdbx_reference_entity_components
Data items in the PDBX_REFERENCE_ENTITY_COMPONENTS category records
sequence of components from which this entity could be built.
Example: 1
<PDBx:pdbx_reference_entity_componentsCategory>
<PDBx:pdbx_reference_entity_components entity_id="1" names="ACE DLY GLY DAL DCY DAS DTY DPR DGL DTR DGN DTR DLE DCY DAL DAL NH2"></PDBx:pdbx_reference_entity_components>
</PDBx:pdbx_reference_entity_componentsCategory>
1
1
pdbx_reference_entity_componentsCategory
This property indicates that datablock
has a category element pdbx_reference_entity_components.
pdbx_reference_entity_componentsItem
Abstract Datatype property for pdbx_reference_entity_components items.
reference_to_pdbx_reference_entity_components
cross-reference to pdbx_reference_entity_components
pdbx_reference_entity_components.entity_id
The value of attribute entity_id in category pdbx_reference_entity_components is a reference
attribute id in category pdbx_reference_entity in the PDBX_REFERENCE_ENTITY category.
pdbx_reference_entity_components.names
The component name list for the entity.
ACE DLY GLY DAL DCY DAS DTY DPR DGL DTR DGN DTR DLE DCY DAL DAL NH2
pdbx_reference_entity_feature
Additional features associated with the reference entity.
Example 1 -
<PDBx:pdbx_reference_entity_featureCategory>
<PDBx:pdbx_reference_entity_feature entity_id="1" source="PDB" type="ENZYME INHIBITED" value="ASPARTIC PROTEINASE"></PDBx:pdbx_reference_entity_feature>
<PDBx:pdbx_reference_entity_feature entity_id="1" source="PDB" type="FUNCTION" value="Transistion-state analogue inhibitor"></PDBx:pdbx_reference_entity_feature>
<PDBx:pdbx_reference_entity_feature entity_id="1" source="IUCR" type="STRUCTURE IMAGE URL" value="http://journals.iucr.org/00X.jpg"></PDBx:pdbx_reference_entity_feature>
</PDBx:pdbx_reference_entity_featureCategory>
0
1
1
1
1
1
pdbx_reference_entity_featureCategory
This property indicates that datablock
has a category element pdbx_reference_entity_feature.
pdbx_reference_entity_featureItem
Abstract Datatype property for pdbx_reference_entity_feature items.
reference_to_pdbx_reference_entity_feature
cross-reference to pdbx_reference_entity_feature
pdbx_reference_entity_feature.support
The supporting evidence for this feature.
Biological assay
Data obtained from PNAS August 17, 1999 vol. 96 no. 17 9586-9590
pdbx_reference_entity_feature.entity_id
The value of attribute entity_id in category pdbx_reference_entity_synonyms is a reference
attribute id in category pdbx_reference_entity in the PDBX_REFERENCE_ENTITY category.
pdbx_reference_entity_feature.source
The information source for the component feature.
PDB
CHEBI
DRUGBANK
PUBCHEM
pdbx_reference_entity_feature.type
The entity feature type.
FUNCTION
ENZYME INHIBITED
STRUCTURE IMAGE URL
pdbx_reference_entity_feature.value
The entity feature value.
pdbx_reference_entity_poly
Data items in the PDBX_REFERENCE_ENTITY_POLY category record details about
the polymer, such as the type of the polymer, the number of
monomers and whether it has nonstandard features.
Example 1 -
<PDBx:pdbx_reference_entity_polyCategory>
<PDBx:pdbx_reference_entity_poly entity_id="1">
<PDBx:nstd_chirality>no</PDBx:nstd_chirality>
<PDBx:nstd_linkage>yes</PDBx:nstd_linkage>
<PDBx:nstd_monomer>yes</PDBx:nstd_monomer>
<PDBx:number_of_monomers>8</PDBx:number_of_monomers>
<PDBx:type>peptide-like</PDBx:type>
</PDBx:pdbx_reference_entity_poly>
</PDBx:pdbx_reference_entity_polyCategory>
0
1
0
1
0
1
0
1
0
1
1
pdbx_reference_entity_polyCategory
This property indicates that datablock
has a category element pdbx_reference_entity_poly.
pdbx_reference_entity_polyItem
Abstract Datatype property for pdbx_reference_entity_poly items.
reference_to_pdbx_reference_entity_poly
cross-reference to pdbx_reference_entity_poly
no
n
yes
y
A flag to indicate whether the polymer contains at least
one monomer unit with non-standard chirality.
no
n
yes
y
A flag to indicate whether the polymer contains at least
one monomer-to-monomer link different from that implied by
attribute type in category pdbx_reference_entity_poly.
no
n
yes
y
A flag to indicate whether the polymer contains at least
one monomer that is not considered standard.
pdbx_reference_entity_poly.number_of_monomers
The number of monomers in the polymer.
pdbx_reference_entity_poly.type
The type of the polymer.
peptide-like
pdbx_reference_entity_poly.entity_id
The value of attribute entity_id in category pdbx_reference_entity_components is a reference
attribute id in category pdbx_reference_entity in the PDBX_REFERENCE_ENTITY category.
pdbx_reference_entity_poly_seq
Data items in the PDBX_REFERENCE_ENTITY_POLY_SEQ category specify the sequence
of monomers in a polymer.
Example 1 -
<PDBx:pdbx_reference_entity_poly_seqCategory>
<PDBx:pdbx_reference_entity_poly_seq entity_id="1" mon_id="PRO" num="1"></PDBx:pdbx_reference_entity_poly_seq>
<PDBx:pdbx_reference_entity_poly_seq entity_id="1" mon_id="GLN" num="2"></PDBx:pdbx_reference_entity_poly_seq>
<PDBx:pdbx_reference_entity_poly_seq entity_id="1" mon_id="ILE" num="3"></PDBx:pdbx_reference_entity_poly_seq>
<PDBx:pdbx_reference_entity_poly_seq entity_id="1" mon_id="THR" num="4"></PDBx:pdbx_reference_entity_poly_seq>
<PDBx:pdbx_reference_entity_poly_seq entity_id="1" mon_id="LEU" num="5"></PDBx:pdbx_reference_entity_poly_seq>
</PDBx:pdbx_reference_entity_poly_seqCategory>
0
1
1
1
1
pdbx_reference_entity_poly_seqCategory
This property indicates that datablock
has a category element pdbx_reference_entity_poly_seq.
pdbx_reference_entity_poly_seqItem
Abstract Datatype property for pdbx_reference_entity_poly_seq items.
reference_to_pdbx_reference_entity_poly_seq
cross-reference to pdbx_reference_entity_poly_seq
pdbx_reference_entity_poly_seq.nstd_mon_parent_id
This data item is the 3-letter-code of the parent of a
non-standard monomer.
ALA
TRP
pdbx_reference_entity_poly_seq.entity_id
The value of attribute entity_id in category pdbx_reference_entity_components is a reference
attribute id in category pdbx_reference_entity in the PDBX_REFERENCE_ENTITY category.
pdbx_reference_entity_poly_seq.mon_id
This data item is the 3-letter-code of monomer.
pdbx_reference_entity_poly_seq.num
The value of attribute num in category pdbx_reference_entity_poly_seq must uniquely and sequentially
identify a record in the PDBX_REFERENCE_ENTITY_POLY_SEQ list.
pdbx_reference_entity_src_nat
Data items in the PDBX_REFERENCE_ENTITY_SRC_NAT category record
details of the source from which the entity was obtained.
Example 1 -
<PDBx:pdbx_reference_entity_src_natCategory>
<PDBx:pdbx_reference_entity_src_nat entity_id="1">
<PDBx:organism_scientific>Mus musculus</PDBx:organism_scientific>
<PDBx:strain></PDBx:strain>
</PDBx:pdbx_reference_entity_src_nat>
</PDBx:pdbx_reference_entity_src_natCategory>
0
1
0
1
1
pdbx_reference_entity_src_natCategory
This property indicates that datablock
has a category element pdbx_reference_entity_src_nat.
pdbx_reference_entity_src_natItem
Abstract Datatype property for pdbx_reference_entity_src_nat items.
reference_to_pdbx_reference_entity_src_nat
cross-reference to pdbx_reference_entity_src_nat
pdbx_reference_entity_src_nat.organism_scientific
The scientific name of the organism from which the entity was isolated.
Mus musculus
pdbx_reference_entity_src_nat.strain
The strain of the organism from which the entity was isolated.
DH5a
BMH 71-18
pdbx_reference_entity_src_nat.entity_id
The value of attribute entity_id in category pdbx_reference_entity_synonyms is a reference
attribute id in category pdbx_reference_entity in the PDBX_REFERENCE_ENTITY category.
pdbx_reference_entity_synonyms
Data items in the PDBX_REFERENCE_ENTITY_SYNONYMS category records
synonym names for reference entities.
Example: 1
<PDBx:pdbx_reference_entity_synonymsCategory>
<PDBx:pdbx_reference_entity_synonyms entity_id="1" name="thiostrepton"></PDBx:pdbx_reference_entity_synonyms>
</PDBx:pdbx_reference_entity_synonymsCategory>
1
1
pdbx_reference_entity_synonymsCategory
This property indicates that datablock
has a category element pdbx_reference_entity_synonyms.
pdbx_reference_entity_synonymsItem
Abstract Datatype property for pdbx_reference_entity_synonyms items.
reference_to_pdbx_reference_entity_synonyms
cross-reference to pdbx_reference_entity_synonyms
pdbx_reference_entity_synonyms.entity_id
The value of attribute entity_id in category pdbx_reference_entity_synonyms is a reference
attribute id in category pdbx_reference_entity in the PDBX_REFERENCE_ENTITY category.
pdbx_reference_entity_synonyms.name
A synonym name for the entity.
thiostrepton
pdbx_refine
Data items in the PDBX_REFINE category record details about
additional structure refinement parameters which are needed
to complete legacy REMARK 3 refinement templates in PDB
format files.
Example 1 - PDB placeholders for refinement program SHELX
<PDBx:pdbx_refineCategory>
<PDBx:pdbx_refine entry_id="ABC001" pdbx_refine_id="x-ray">
<PDBx:R_factor_all_4sig_cutoff>0.174</PDBx:R_factor_all_4sig_cutoff>
<PDBx:R_factor_obs_4sig_cutoff>0.169</PDBx:R_factor_obs_4sig_cutoff>
<PDBx:free_R_factor_4sig_cutoff>0.216</PDBx:free_R_factor_4sig_cutoff>
<PDBx:free_R_val_test_set_ct_4sig_cutoff>164</PDBx:free_R_val_test_set_ct_4sig_cutoff>
<PDBx:free_R_val_test_set_size_perc_4sig_cutoff>1.29</PDBx:free_R_val_test_set_size_perc_4sig_cutoff>
<PDBx:number_reflns_obs_4sig_cutoff>1263</PDBx:number_reflns_obs_4sig_cutoff>
</PDBx:pdbx_refine>
</PDBx:pdbx_refineCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
pdbx_refineCategory
This property indicates that datablock
has a category element pdbx_refine.
pdbx_refineItem
Abstract Datatype property for pdbx_refine items.
reference_to_pdbx_refine
cross-reference to pdbx_refine
pdbx_refine.R_factor_all_4sig_cutoff
R-value (all reflections, 4 sigma cutoff)
Placeholder for PDB mapping of SHELXL refinement data.
0.174
pdbx_refine.R_factor_all_no_cutoff
R-value (all reflections, no cutoff)
Placeholder for PDB mapping of SHELXL refinement data.
pdbx_refine.R_factor_obs_4sig_cutoff
R-value (working set, 4 sigma cutoff)
Placeholder for PDB mapping of SHELXL refinement data.
0.169
pdbx_refine.R_factor_obs_no_cutoff
R-value (working set reflections, no cutoff)
Placeholder for PDB mapping of SHELXL refinement data.
pdbx_refine.free_R_error_no_cutoff
Free R-value error(no cutoff)
pdbx_refine.free_R_factor_4sig_cutoff
R free value (4 sigma cutoff).
Placeholder for PDB mapping of SHELXL refinement data.
0.216
pdbx_refine.free_R_factor_no_cutoff
Free R-value (no cutoff)
Placeholder for PDB mapping of SHELXL refinement data.
pdbx_refine.free_R_val_4sig_cutoff
Free R-value (4 sigma cutoff)
Placeholder for PDB mapping of SHELXL refinement data.
pdbx_refine.free_R_val_test_set_ct_4sig_cutoff
Free R-value test set count (4 sigma cutoff)
Placeholder for PDB mapping of SHELXL refinement data.
164
pdbx_refine.free_R_val_test_set_ct_no_cutoff
Free R-value test set count (no cutoff)
Placeholder for PDB mapping of SHELXL refinement data.
pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff
Free R-value test set size (in percent, 4 sigma cutoff)
Placeholder for PDB mapping of SHELXL refinement data.
1.29
pdbx_refine.free_R_val_test_set_size_perc_no_cutoff
Free R-value test set size (in percent, no cutoff)
Placeholder for PDB mapping of SHELXL refinement data.
pdbx_refine.number_reflns_obs_4sig_cutoff
Total number of reflections (4 sigma cutoff).
Placeholder for PDB mapping of SHELXL refinement data.
1263
pdbx_refine.number_reflns_obs_no_cutoff
Total number of reflections (no cutoff).
Placeholder for PDB mapping of SHELXL refinement data.
pdbx_refine.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
pdbx_refine.pdbx_refine_id
This data item uniquely identifies a refinement within an entry.
attribute pdbx_refine_id in category pdbx_refine can be used to distinguish the results
of joint refinements.
pdbx_refine_aux_file
Auxilary parameter and topology files used in refinement.
<PDBx:pdbx_refine_aux_fileCategory>
<PDBx:pdbx_refine_aux_file pdbx_refine_id="x-ray" serial_no="1">
<PDBx:file_name>parm_hol.dat</PDBx:file_name>
<PDBx:file_type>PARAMETER</PDBx:file_type>
</PDBx:pdbx_refine_aux_file>
</PDBx:pdbx_refine_aux_fileCategory>
0
1
0
1
1
1
pdbx_refine_aux_fileCategory
This property indicates that datablock
has a category element pdbx_refine_aux_file.
pdbx_refine_aux_fileItem
Abstract Datatype property for pdbx_refine_aux_file items.
reference_to_pdbx_refine_aux_file
cross-reference to pdbx_refine_aux_file
pdbx_refine_aux_file.file_name
Auxilary file name.
PARAM_NDBX_HIGH.DNA
PARAMETER
TOPOLOGY
Auxilary file type.
PARAMETER
pdbx_refine_aux_file.pdbx_refine_id
This data item uniquely identifies a refinement within an entry.
attribute pdbx_refine_id in category pdbx_refine_aux_file can be used to distinguish the results
of joint refinements.
pdbx_refine_aux_file.serial_no
Serial number.
pdbx_refine_component
Data items in the PDBX_REFINE_COMPONENT category record
statistics of the final model relative to the density map.
Example 1 -
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
pdbx_refine_componentCategory
This property indicates that datablock
has a category element pdbx_refine_component.
pdbx_refine_componentItem
Abstract Datatype property for pdbx_refine_component items.
reference_to_pdbx_refine_component
cross-reference to pdbx_refine_component
pdbx_refine_component.B_iso
The average isotropic B factors for the group of atoms
(e.g. residue or ligand, side chain, main chain).
The B factors for each atom is given by attribute B_iso_or_equiv in category atom_site
pdbx_refine_component.B_iso_main_chain
The average isotropic B factors for the group of atoms
(e.g. residue or ligand, side chain, main chain).
The B factors for each atom is given by attribute B_iso_or_equiv in category atom_site
pdbx_refine_component.B_iso_side_chain
The average isotropic B factors for the group of atoms
(e.g. residue or ligand, side chain, main chain).
The B factors for each atom is given by attribute B_iso_or_equiv in category atom_site
pdbx_refine_component.PDB_ins_code
A component of the identifier for the component.
This data item is a pointer to attribute pdbx_PDB_ins_code
in category atom_site ATOM_SITE category.
pdbx_refine_component.auth_asym_id
A component of the identifier for the component.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_refine_component.auth_comp_id
A component of the identifier for the component.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_refine_component.auth_seq_id
A component of the identifier for the component.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_refine_component.connect
The index of connectivity is the product of the (2Fobs-Fcal) electron
density values for the backbone atoms (N, CA and C) divided by the
average value for the structure. Low values (less than 1.0) of this
index indicate breaks in the backbone electron density which may be
due to flexibility of the chain or incorrect tracing.
connect = [(D(xi)...D(xi))^(1/N)] /<D>_all
Where:
D(xi) = (2*Fobs - Fcal)
<D>_all is the averaged value of density for the structure.
The product is for N atoms of group.
Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205
pdbx_refine_component.correlation
Correlation coefficient of electron density for each residue or ligand,
side chain, main chain
The density correlation coefficient is calculated for each component
from atomic densities of (2Fobs-Fcalc) map - "Robs" and the model
map (Fcalc) - "Rcalc" :
D_corr = <Robs><Rcalc>/sqrt(<Robs**2><Rcalc**2>)
where <Robs> is the mean of "observed" densities of atoms of the
component (backbone or side chain).
<Rcalc> is the mean of "calculated" densities of
component atoms.
The value of density for some atom from map R(x) is:
sum_i ( R(xi) * Ratom(xi - xa) )
Dens = ----------------------------------
sum_i ( Ratom(xi - xa) )
where Ratom(x) is atomic electron density for the x-th grid point.
xa - vector of the centre of atom.
xi - vector of the i-th point of grid.
Sum is taken over all grid points which have distance
from the center of the atom less than the Radius_limit.
For all atoms Radius_limit = 2.5 A.
Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205
pdbx_refine_component.correlation_main_chain
Correlation coefficient of electron density for each residue or ligand,
side chain, main chain
The density correlation coefficient is calculated for each component
from atomic densities of (2Fobs-Fcalc) map - "Robs" and the model
map (Fcalc) - "Rcalc" :
D_corr = <Robs><Rcalc>/sqrt(<Robs**2><Rcalc**2>)
where <Robs> is the mean of "observed" densities of atoms of the
component (backbone or side chain).
<Rcalc> is the mean of "calculated" densities of
component atoms.
The value of density for some atom from map R(x) is:
sum_i ( R(xi) * Ratom(xi - xa) )
Dens = ----------------------------------
sum_i ( Ratom(xi - xa) )
where Ratom(x) is atomic electron density for the x-th grid point.
xa - vector of the centre of atom.
xi - vector of the i-th point of grid.
Sum is taken over all grid points which have distance
from the center of the atom less than the Radius_limit.
For all atoms Radius_limit = 2.5 A.
Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205
pdbx_refine_component.correlation_side_chain
Correlation coefficient of electron density for each residue or ligand,
side chain, main chain
The density correlation coefficient is calculated for each component
from atomic densities of (2Fobs-Fcalc) map - "Robs" and the model
map (Fcalc) - "Rcalc" :
D_corr = <Robs><Rcalc>/sqrt(<Robs**2><Rcalc**2>)
where <Robs> is the mean of "observed" densities of atoms of the
component (backbone or side chain).
<Rcalc> is the mean of "calculated" densities of
component atoms.
The value of density for some atom from map R(x) is:
sum_i ( R(xi) * Ratom(xi - xa) )
Dens = ----------------------------------
sum_i ( Ratom(xi - xa) )
where Ratom(x) is atomic electron density for the x-th grid point.
xa - vector of the centre of atom.
xi - vector of the i-th point of grid.
Sum is taken over all grid points which have distance
from the center of the atom less than the Radius_limit.
For all atoms Radius_limit = 2.5 A.
Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205
pdbx_refine_component.density_index
The index of density is the product of the (2Fobs-Fcal) electron
density values for the group of atoms divided by the average value
for the structure. Low values (less than 1.0) may be problematic for
model fitting.
index = [(D(xi)...D(xi))^(1/N)] /<D>_all
Where :
D(xi) = (2*Fobs - Fcal)
<D>_all is the averaged value of density for the structure.
The product is for N atoms of group.
Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205
pdbx_refine_component.density_index_main_chain
The index of density is the product of the (2Fobs-Fcal) electron
density values for the group of atoms divided by the average value
for the structure. Low values (less than 1.0) may be problematic for
model fitting.
index = [(D(xi)...D(xi))^(1/N)] /<D>_all
Where :
D(xi) = (2*Fobs - Fcal)
<D>_all is the averaged value of density for the structure.
The product is for N atoms of group.
Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205
pdbx_refine_component.density_index_side_chain
The index of density is the product of the (2Fobs-Fcal) electron
density values for the group of atoms divided by the average value
for the structure. Low values (less than 1.0) may be problematic for
model fitting.
index = [(D(xi)...D(xi))^(1/N)] /<D>_all
Where :
D(xi) = (2*Fobs - Fcal)
<D>_all is the averaged value of density for the structure.
The product is for N atoms of group.
Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205
pdbx_refine_component.density_ratio
The density ratio is similar to the density index, but summation of the
density for the group is used for calculation.
The ratio of density is the summation of the (2Fobs-Fcal) electron
density values for the group of atoms divided by the average value
for the structure. Low values (less than 0.4) of this ratio may be
problematic for the group.
index = [Sum~i D(xi)]/<D>_all
Where:
D(xi) = (2*Fobs - Fcal)
<D>_all is the average value of density for the structure.
The summation is for all the atoms of group.
pdbx_refine_component.density_ratio_main_chain
The density ratio is similar to the density index, but summation of the
density for the group is used for calculation.
The ratio of density is the summation of the (2Fobs-Fcal) electron
density values for the group of atoms divided by the average value
for the structure. Low values (less than 0.4) of this ratio may be
problematic for the group.
index = [Sum~i D(xi)]/<D>_all
Where:
D(xi) = (2*Fobs - Fcal)
<D>_all is the average value of density for the structure.
The summation is for all the atoms of group.
pdbx_refine_component.density_ratio_side_chain
The density ratio is similar to the density index, but summation of the
density for the group is used for calculation.
The ratio of density is the summation of the (2Fobs-Fcal) electron
density values for the group of atoms divided by the average value
for the structure. Low values (less than 0.4) of this ratio may be
problematic for the group.
index = [Sum~i D(xi)]/<D>_all
Where:
D(xi) = (2*Fobs - Fcal)
<D>_all is the average value of density for the structure.
The summation is for all the atoms of group.
pdbx_refine_component.real_space_R
Real space R factor of electron density for each component,
residue side chain, or main chain.
The real space R factor is calculated by the equation
R_real = [Sum~i (|Dobs - Dcal|)]/[Sum~i (|Dobs + Dcal|)]
Where:
Dobs is the observed electron density,
Dcal is the calculated electron density,
summation is for all the grid points
Ref: Branden, C.I. & Jones, T.A. (1990). Nature, 343, 687-689
pdbx_refine_component.real_space_R_main_chain
Real space R factor of electron density for each component,
residue side chain, or main chain.
The real space R factor is calculated by the equation
R_real = [Sum~i (|Dobs - Dcal|)]/[Sum~i (|Dobs + Dcal|)]
Where:
Dobs is the observed electron density,
Dcal is the calculated electron density,
summation is for all the grid points
Ref: Branden, C.I. & Jones, T.A. (1990). Nature, 343, 687-689
pdbx_refine_component.real_space_R_side_chain
Real space R factor of electron density for each component,
residue side chain, or main chain.
The real space R factor is calculated by the equation
R_real = [Sum~i (|Dobs - Dcal|)]/[Sum~i (|Dobs + Dcal|)]
Where:
Dobs is the observed electron density,
Dcal is the calculated electron density,
summation is for all the grid points
Ref: Branden, C.I. & Jones, T.A. (1990). Nature, 343, 687-689
pdbx_refine_component.shift
The tendency of the group of atoms (e.g. residue
or ligand, side chain, main chain) to move away from its current position.
Displacement of atoms from electron density is estimated from the
difference (Fobs - Fcal) map. The displacement vector is the ratio of
the gradient of difference density to the curvature. The amplitude of
the displacement vector is an indicator of the positional error.
Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205
pdbx_refine_component.shift_main_chain
The tendency of the group of atoms (e.g. residue
or ligand, side chain, main chain) to move away from its current position.
Displacement of atoms from electron density is estimated from the
difference (Fobs - Fcal) map. The displacement vector is the ratio of
the gradient of difference density to the curvature. The amplitude of
the displacement vector is an indicator of the positional error.
Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205
pdbx_refine_component.shift_side_chain
The tendency of the group of atoms (e.g. residue
or ligand, side chain, main chain) to move away from its current position.
Displacement of atoms from electron density is estimated from the
difference (Fobs - Fcal) map. The displacement vector is the ratio of
the gradient of difference density to the curvature. The amplitude of
the displacement vector is an indicator of the positional error.
Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205
pdbx_refine_component.label_alt_id
A component of the identifier for the component.
This data item is a pointer to attribute id in category atom_sites_alt in the
ATOM_SITES_ALT category.
pdbx_refine_component.label_asym_id
A component of the identifier for the component.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_refine_component.label_comp_id
A component of the identifier for the component.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_refine_component.label_seq_id
A component of the identifier for the component.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_refine_tls
Data items in the REFINE_TLS category record details about
TLS parameters used in structure refinement. Note that the
intention is primarily to describe directly refined TLS
parameters, although other methods of obtaining TLS parameters
may be covered, see item attribute method in category pdbx_refine_tls
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
pdbx_refine_tlsCategory
This property indicates that datablock
has a category element pdbx_refine_tls.
pdbx_refine_tlsItem
Abstract Datatype property for pdbx_refine_tls items.
reference_to_pdbx_refine_tls
cross-reference to pdbx_refine_tls
pdbx_refine_tls.L11
The [1][1] element of the libration tensor L. This should
be given in the same coordinate frame as the
corresponding anisotropic displacement parameters.
pdbx_refine_tls.L11_esd
The estimated standard deviation of attribute L[1][1] in category pdbx_refine_tls.
pdbx_refine_tls.L12
The [1][2] element of the libration tensor L. This should
be given in the same coordinate frame as the
corresponding anisotropic displacement parameters.
pdbx_refine_tls.L12_esd
The estimated standard deviation of attribute L[1][2] in category pdbx_refine_tls.
pdbx_refine_tls.L13
The [1][3] element of the libration tensor L. This should
be given in the same coordinate frame as the
corresponding anisotropic displacement parameters.
pdbx_refine_tls.L13_esd
The estimated standard deviation of attribute L[1][3] in category pdbx_refine_tls.
pdbx_refine_tls.L22
The [2][2] element of the libration tensor L. This should
be given in the same coordinate frame as the
corresponding anisotropic displacement parameters.
pdbx_refine_tls.L22_esd
The estimated standard deviation of attribute L[2][2] in category pdbx_refine_tls.
pdbx_refine_tls.L23
The [2][3] element of the libration tensor L. This should
be given in the same coordinate frame as the
corresponding anisotropic displacement parameters.
pdbx_refine_tls.L23_esd
The estimated standard deviation of attribute L[2][3] in category pdbx_refine_tls.
pdbx_refine_tls.L33
The [3][3] element of the libration tensor L. This should
be given in the same coordinate frame as the
corresponding anisotropic displacement parameters.
pdbx_refine_tls.L33_esd
The estimated standard deviation of attribute L[3][3] in category pdbx_refine_tls.
pdbx_refine_tls.S11
The [1][1] element of the screw-rotation tensor S. This should
be given in the same coordinate frame as the
corresponding anisotropic displacement parameters.
The trace of S is indeterminate by crystallography, and should
be set to zero.
pdbx_refine_tls.S11_esd
The estimated standard deviation of attribute S[1][1] in category pdbx_refine_tls.
pdbx_refine_tls.S12
The [1][2] element of the screw-rotation tensor S. This should
be given in the same coordinate frame as the
corresponding anisotropic displacement parameters.
If the origin is omitted, it is assumed to be the centre of
reaction of the group, in which case S must be symmetric
pdbx_refine_tls.S12_esd
The estimated standard deviation of attribute S[1][2] in category pdbx_refine_tls.
pdbx_refine_tls.S13
The [1][3] element of the screw-rotation tensor S. This should
be given in the same coordinate frame as the
corresponding anisotropic displacement parameters.
If the origin is omitted, it is assumed to be the centre of
reaction of the group, in which case S must be symmetric
pdbx_refine_tls.S13_esd
The estimated standard deviation of attribute S[1][3] in category pdbx_refine_tls.
pdbx_refine_tls.S21
The [2][1] element of the screw-rotation tensor S. This should
be given in the same coordinate frame as the
corresponding anisotropic displacement parameters.
If the origin is omitted, it is assumed to be the centre of
reaction of the group, in which case S must be symmetric
pdbx_refine_tls.S21_esd
The estimated standard deviation of attribute S[2][1] in category pdbx_refine_tls.
pdbx_refine_tls.S22
The [2][2] element of the screw-rotation tensor S. This should
be given in the same coordinate frame as the
corresponding anisotropic displacement parameters.
The trace of S is indeterminate by crystallography, and should
be set to zero.
pdbx_refine_tls.S22_esd
The estimated standard deviation of attribute S[2][2] in category pdbx_refine_tls.
pdbx_refine_tls.S23
The [2][3] element of the screw-rotation tensor S. This should
be given in the same coordinate frame as the
corresponding anisotropic displacement parameters.
If the origin is omitted, it is assumed to be the centre of
reaction of the group, in which case S must be symmetric
pdbx_refine_tls.S23_esd
The estimated standard deviation of attribute S[2][3] in category pdbx_refine_tls.
pdbx_refine_tls.S31
The [3][1] element of the screw-rotation tensor S. This should
be given in the same coordinate frame as the
corresponding anisotropic displacement parameters.
If the origin is omitted, it is assumed to be the centre of
reaction of the group, in which case S must be symmetric
pdbx_refine_tls.S31_esd
The estimated standard deviation of attribute S[3][1] in category pdbx_refine_tls.
pdbx_refine_tls.S32
The [3][2] element of the screw-rotation tensor S. This should
be given in the same coordinate frame as the
corresponding anisotropic displacement parameters.
If the origin is omitted, it is assumed to be the centre of
reaction of the group, in which case S must be symmetric
pdbx_refine_tls.S32_esd
The estimated standard deviation of attribute S[3][2] in category pdbx_refine_tls.
pdbx_refine_tls.S33
The [3][3] element of the screw-rotation tensor S. This should
be given in the same coordinate frame as the
corresponding anisotropic displacement parameters.
The trace of S is indeterminate by crystallography, and should
be set to zero.
pdbx_refine_tls.S33_esd
The estimated standard deviation of attribute S[3][3] in category pdbx_refine_tls.
pdbx_refine_tls.T11
The [1][1] element of the translation tensor T. This should
be given in the same coordinate frame and units as the
corresponding anisotropic displacement parameters.
pdbx_refine_tls.T11_esd
The estimated standard deviation of attribute T[1][1] in category pdbx_refine_tls.
pdbx_refine_tls.T12
The [1][2] element of the translation tensor T. This should
be given in the same coordinate frame and units as the
corresponding anisotropic displacement parameters.
pdbx_refine_tls.T12_esd
The estimated standard deviation of attribute T[1][2] in category pdbx_refine_tls.
pdbx_refine_tls.T13
The [1][3] element of the translation tensor T. This should
be given in the same coordinate frame and units as the
corresponding anisotropic displacement parameters.
pdbx_refine_tls.T13_esd
The estimated standard deviation of attribute T[1][3] in category pdbx_refine_tls.
pdbx_refine_tls.T22
The [2][2] element of the translation tensor T. This should
be given in the same coordinate frame and units as the
corresponding anisotropic displacement parameters.
pdbx_refine_tls.T22_esd
The estimated standard deviation of attribute T[2][2] in category pdbx_refine_tls.
pdbx_refine_tls.T23
The [2][3] element of the translation tensor T. This should
be given in the same coordinate frame and units as the
corresponding anisotropic displacement parameters.
pdbx_refine_tls.T23_esd
The estimated standard deviation of attribute T[2][3] in category pdbx_refine_tls.
pdbx_refine_tls.T33
The [3][3] element of the translation tensor T. This should
be given in the same coordinate frame and units as the
corresponding anisotropic displacement parameters.
pdbx_refine_tls.T33_esd
The estimated standard deviation of attribute T[3][3] in category pdbx_refine_tls.
pdbx_refine_tls.details
A description of the TLS group, such as a domain name or a
chemical group name.
Chain A catalytic domain
Chain A Tyr 56 side chain
refined
fitted
The method by which the TLS parameters were obtained.
pdbx_refine_tls.origin_x
The x coordinate in angstroms of the origin to which the
TLS parameters are referred, specified according to
a set of orthogonal Cartesian axes related to the cell axes as
given in attribute Cartn_transform_axes.
in category atom_sites
If the origin is omitted, it is assumed to be the centre of
reaction of the group, in which case S must be symmetric
pdbx_refine_tls.origin_y
The y coordinate in angstroms of the origin to which the
TLS parameters are referred, specified according to
a set of orthogonal Cartesian axes related to the cell axes as
given in attribute Cartn_transform_axes.
in category atom_sites
If the origin is omitted, it is assumed to be the centre of
reaction of the group, in which case S must be symmetric
pdbx_refine_tls.origin_z
The z coordinate in angstroms of the origin to which the
TLS parameters are referred, specified according to
a set of orthogonal Cartesian axes related to the cell axes as
given in attribute Cartn_transform_axes.
in category atom_sites
If the origin is omitted, it is assumed to be the centre of
reaction of the group, in which case S must be symmetric
pdbx_refine_tls.pdbx_refine_id
This data item uniquely identifies a refinement within an entry.
attribute pdbx_refine_id in category pdbx_refine_tls can be used to distinguish the results
of joint refinements.
pdbx_refine_tls.id
The value of attribute id in category pdbx_refine_tls must uniquely identify a record in
the PDBX_REFINE_TLS list.
Note that this item need not be a number; it can be any unique
identifier.
1
A
pdbx_refine_tls_group
Data items in the PDBX_REFINE_TLS_GROUP category record details about
a fragment of a TLS group.
Properties of the TLS group are recorded in PDBX_REFINE_TLS
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
0
1
0
1
1
pdbx_refine_tls_groupCategory
This property indicates that datablock
has a category element pdbx_refine_tls_group.
pdbx_refine_tls_groupItem
Abstract Datatype property for pdbx_refine_tls_group items.
reference_to_pdbx_refine_tls_group
cross-reference to pdbx_refine_tls_group
pdbx_refine_tls_group.beg_auth_asym_id
A component of the identifier for the residue at which the
TLS fragment range begins.
O
2B3
pdbx_refine_tls_group.beg_auth_seq_id
A component of the identifier for the residue at which the
TLS fragment range begins.
1
5A
pdbx_refine_tls_group.beg_label_asym_id
A component of the identifier for the residue at which the
TLS fragment range begins.
This data item is a pointer to attribute id in category struct_asym in the
STRUCT_ASYM category.
O
2B3
pdbx_refine_tls_group.beg_label_seq_id
A component of the identifier for the residue at which the
TLS fragment range begins.
1
303
pdbx_refine_tls_group.end_auth_asym_id
A component of the identifier for the residue at which the
TLS fragment range ends.
O
2B3
pdbx_refine_tls_group.end_auth_seq_id
A component of the identifier for the residue at which the
TLS fragment range ends.
1
5A
pdbx_refine_tls_group.end_label_asym_id
A component of the identifier for the residue at which the
TLS fragment range ends.
This data item is a pointer to attribute id in category struct_asym in the
STRUCT_ASYM category.
O
2B3
pdbx_refine_tls_group.end_label_seq_id
A component of the identifier for the residue at which the
TLS fragment range ends.
1
303
pdbx_refine_tls_group.pdbx_refine_id
This data item uniquely identifies a refinement within an entry.
attribute pdbx_refine_id in category pdbx_refine_tls_group can be used to distinguish the results
of joint refinements.
pdbx_refine_tls_group.refine_tls_id
This data item is a pointer to attribute id in category pdbx_refine_tls in the
REFINE_TLS category.
pdbx_refine_tls_group.selection
A qualification of the subset of atoms in the specified
range included in the TLS fragment.
all atoms in specified range
all
main chain atoms only
mnc
side chain atoms only
sdc
pdbx_refine_tls_group.selection_details
A text description of subset of atoms included
included in the TLS fragment.
pdbx_refine_tls_group.id
The value of attribute id in category pdbx_refine_tls_group must uniquely identify
a record in the REFINE_TLS_GROUP list for a particular refinement.
Note that this item need not be a number; it can be any unique
identifier.
1
A
pdbx_reflns_twin
Details decribing crystallographic twinning.
Example 1 -
<PDBx:pdbx_reflns_twinCategory>
<PDBx:pdbx_reflns_twin crystal_id="1" diffrn_id="1" operator="h,-h-k,-l">
<PDBx:fraction>.43</PDBx:fraction>
<PDBx:mean_F_square_over_mean_F2>.84</PDBx:mean_F_square_over_mean_F2>
<PDBx:mean_I2_over_mean_I_square>1.3</PDBx:mean_I2_over_mean_I_square>
<PDBx:type>merohedral</PDBx:type>
</PDBx:pdbx_reflns_twin>
</PDBx:pdbx_reflns_twinCategory>
0
1
1
1
0
1
0
1
0
1
1
1
1
pdbx_reflns_twinCategory
This property indicates that datablock
has a category element pdbx_reflns_twin.
pdbx_reflns_twinItem
Abstract Datatype property for pdbx_reflns_twin items.
reference_to_pdbx_reflns_twin
cross-reference to pdbx_reflns_twin
pdbx_reflns_twin.domain_id
An identifier for the twin domain.
pdbx_reflns_twin.fraction
The twin fraction or twin factor represents a quantitative parameter for the
crystal twinning. The value 0 represents no twinning, < 0.5 partial twinning,
= 0.5 for perfect twinning.
pdbx_reflns_twin.mean_F_square_over_mean_F2
The ideal statistics for twinned crystals. The values calculated with the
acentric data are given below.
Statistic Untwinned data Perfect twinned data
<I^2>/<I>^2 2.0 1.5
<F>^2/<F^2> 0.785 0.865
References:
Yeates, T.O. (1997) Methods in Enzymology 276, 344-358. Detecting and
Overcoming Crystal Twinning.
and information from the following on-line sites:
CNS site http://cns.csb.yale.edu/v1.1/
CCP4 site http://www.ccp4.ac.uk/dist/html/detwin.html
SHELX site http://shelx.uni-ac.gwdg.de/~rherbst/twin.html
pdbx_reflns_twin.mean_I2_over_mean_I_square
The ideal statistics for twinned crystals. The values calculated with the
acentric data are given below.
Statistic Untwinned data Perfect twinned data
<I^2>/<I>^2 2.0 1.5
<F>^2/<F^2> 0.785 0.865
References:
Yeates, T.O. (1997) Methods in Enzymology 276, 344-358. Detecting and
Overcoming Crystal Twinning.
and information from the following on-line sites:
CNS site http://cns.csb.yale.edu/v1.1/
CCP4 site http://www.ccp4.ac.uk/dist/html/detwin.html
SHELX site http://shelx.uni-ac.gwdg.de/~rherbst/twin.html
merohedral
hemihedral
non-merohedral
pseudo-merohedral
epitaxial
tetartohedral
There are two types of twinning: merohedral or hemihedral
non-merohedral or epitaxial
For merohedral twinning the diffraction patterns from the different domains are
completely superimposable. Hemihedral twinning is a special case of merohedral
twinning. It only involves two distinct domains. Pseudo-merohedral twinning is
a subclass merohedral twinning in which lattice is coincidentally superimposable.
In the case of non-merohedral or epitaxial twinning the reciprocal
lattices do not superimpose exactly. In this case the diffraction pattern
consists of two (or more) interpenetrating lattices, which can in principle
be separated.
pdbx_reflns_twin.crystal_id
The crystal identifier. A reference to
attribute id in category exptl_crystal in category EXPTL_CRYSTAL.
pdbx_reflns_twin.diffrn_id
The diffraction data set identifier. A reference to
attribute id in category diffrn in category DIFFRN.
pdbx_reflns_twin.operator
The possible merohedral or hemihedral twinning operators for different
point groups are:
True point group Twin operation hkl related to
3 2 along a,b h,-h-k,-l
2 along a*,b* h+k,-k,-l
2 along c -h,-k,l
4 2 along a,b,a*,b* h,-k,-l
6 2 along a,b,a*,b* h,-h-k,-l
321 2 along a*,b*,c -h,-k,l
312 2 along a,b,c -h,-k,l
23 4 along a,b,c k,-h,l
References:
Yeates, T.O. (1997) Methods in Enzymology 276, 344-358. Detecting and
Overcoming Crystal Twinning.
and information from the following on-line sites:
CNS site http://cns.csb.yale.edu/v1.1/
CCP4 site http://www.ccp4.ac.uk/dist/html/detwin.html
SHELX site http://shelx.uni-ac.gwdg.de/~rherbst/twin.html
h,-h-k,-l
h+k,-k,-l
-h,-k,l
h,-k,-l
k,-h,l
pdbx_remediation_atom_site_mapping
Data items in the PDBX_REMEDIATION_ATOM_SITE_MAPPING category records
mapping information between selected molecular entities that have been
chemically redefined. The prior and current atom nomenclature is
tabulated in this category.
Example component QUA
<PDBx:pdbx_remediation_atom_site_mappingCategory>
<PDBx:pdbx_remediation_atom_site_mapping id="1">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:auth_alt_id></PDBx:auth_alt_id>
<PDBx:auth_asym_id>C</PDBx:auth_asym_id>
<PDBx:auth_atom_id>O12</PDBx:auth_atom_id>
<PDBx:auth_comp_id>QUA</PDBx:auth_comp_id>
<PDBx:auth_seq_id>7</PDBx:auth_seq_id>
<PDBx:group_PDB>HETATM</PDBx:group_PDB>
<PDBx:label_alt_id></PDBx:label_alt_id>
<PDBx:label_asym_id>C</PDBx:label_asym_id>
<PDBx:label_atom_id>O12</PDBx:label_atom_id>
<PDBx:label_comp_id>QUA</PDBx:label_comp_id>
<PDBx:label_seq_id>0</PDBx:label_seq_id>
<PDBx:pdbx_align>1</PDBx:pdbx_align>
<PDBx:pre_PDB_ins_code></PDBx:pre_PDB_ins_code>
<PDBx:pre_auth_alt_id></PDBx:pre_auth_alt_id>
<PDBx:pre_auth_asym_id>C</PDBx:pre_auth_asym_id>
<PDBx:pre_auth_atom_id>O12</PDBx:pre_auth_atom_id>
<PDBx:pre_auth_comp_id>QUA</PDBx:pre_auth_comp_id>
<PDBx:pre_auth_seq_id>7</PDBx:pre_auth_seq_id>
<PDBx:pre_group_PDB>HETATM</PDBx:pre_group_PDB>
<PDBx:pre_pdbx_align>1</PDBx:pre_pdbx_align>
</PDBx:pdbx_remediation_atom_site_mapping>
<PDBx:pdbx_remediation_atom_site_mapping id="2">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:auth_alt_id></PDBx:auth_alt_id>
<PDBx:auth_asym_id>C</PDBx:auth_asym_id>
<PDBx:auth_atom_id>C11</PDBx:auth_atom_id>
<PDBx:auth_comp_id>QUA</PDBx:auth_comp_id>
<PDBx:auth_seq_id>7</PDBx:auth_seq_id>
<PDBx:group_PDB>HETATM</PDBx:group_PDB>
<PDBx:label_alt_id></PDBx:label_alt_id>
<PDBx:label_asym_id>C</PDBx:label_asym_id>
<PDBx:label_atom_id>C11</PDBx:label_atom_id>
<PDBx:label_comp_id>QUA</PDBx:label_comp_id>
<PDBx:label_seq_id>0</PDBx:label_seq_id>
<PDBx:pdbx_align>1</PDBx:pdbx_align>
<PDBx:pre_PDB_ins_code></PDBx:pre_PDB_ins_code>
<PDBx:pre_auth_alt_id></PDBx:pre_auth_alt_id>
<PDBx:pre_auth_asym_id>C</PDBx:pre_auth_asym_id>
<PDBx:pre_auth_atom_id>C11</PDBx:pre_auth_atom_id>
<PDBx:pre_auth_comp_id>QUA</PDBx:pre_auth_comp_id>
<PDBx:pre_auth_seq_id>7</PDBx:pre_auth_seq_id>
<PDBx:pre_group_PDB>HETATM</PDBx:pre_group_PDB>
<PDBx:pre_pdbx_align>1</PDBx:pre_pdbx_align>
</PDBx:pdbx_remediation_atom_site_mapping>
</PDBx:pdbx_remediation_atom_site_mappingCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
1
1
1
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
pdbx_remediation_atom_site_mappingCategory
This property indicates that datablock
has a category element pdbx_remediation_atom_site_mapping.
pdbx_remediation_atom_site_mappingItem
Abstract Datatype property for pdbx_remediation_atom_site_mapping items.
reference_to_pdbx_remediation_atom_site_mapping
cross-reference to pdbx_remediation_atom_site_mapping
pdbx_remediation_atom_site_mapping.PDB_ins_code
Optional atom_site identifier.
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the
ATOM_SITE category.
pdbx_remediation_atom_site_mapping.auth_alt_id
A component of the current atom_site identifier.
This data item is a pointer to attribute pdbx_auth_alt_id in category atom_site in the
ATOM_SITE category.
pdbx_remediation_atom_site_mapping.auth_asym_id
A component of the current atom_site identifier.
This data item corresponds to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_remediation_atom_site_mapping.auth_atom_id
A component of the current atom_site identifier.
This data item corrresponds to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
pdbx_remediation_atom_site_mapping.auth_comp_id
A component of the current atom_site identifier.
This data item corresponds to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_remediation_atom_site_mapping.auth_seq_id
A component of the current atom_site identifier.
This data item corresponds to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
ATOM
HETATM
The PDB group of atoms to which the atom site belongs.
pdbx_remediation_atom_site_mapping.label_alt_id
A component of the atom_site identifier.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
pdbx_remediation_atom_site_mapping.label_asym_id
A component of the atom_site identifier.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_remediation_atom_site_mapping.label_atom_id
A component of the atom_site identifier.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
pdbx_remediation_atom_site_mapping.label_comp_id
A component of the atom_site identifier.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_remediation_atom_site_mapping.label_seq_id
A component of the atom_site identifier.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_remediation_atom_site_mapping.occupancy
The fraction of the atom type present at the current atom site.
pdbx_remediation_atom_site_mapping.pdbx_align
An optional alignment flag.
pdbx_remediation_atom_site_mapping.pre_PDB_ins_code
A component of the prior atom_site identifier.
This data item corresponds to attribute pdbx_PDB_ins_code in category atom_site in the
ATOM_SITE category.
pdbx_remediation_atom_site_mapping.pre_auth_alt_id
A component of the prior atom_site identifier.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
pdbx_remediation_atom_site_mapping.pre_auth_asym_id
A component of the prior atom_site identifier.
This data item corresponds to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_remediation_atom_site_mapping.pre_auth_atom_id
A component of the prior atom_site identifier.
This data item corrresponds to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
pdbx_remediation_atom_site_mapping.pre_auth_comp_id
A component of the prior atom_site identifier.
This data item corresponds to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_remediation_atom_site_mapping.pre_auth_seq_id
A component of the prior atom_site identifier.
This data item corresponds to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
ATOM
HETATM
A component of the prior atom_site identifier.
This item corresponds to the PDB group of atoms to which the atom site belongs.
pdbx_remediation_atom_site_mapping.pre_occupancy
The fraction of the atom type present for the prior atom site.
pdbx_remediation_atom_site_mapping.pre_pdbx_align
An optional alignment flag.
pdbx_remediation_atom_site_mapping.id
The value of pdbx_remediation_atom_site_mapping.id must uniquely identify a record in
the PDBX_REMEDIATION_ATOM_SITE_MAPPING list.
Note that this item need not be a number; it can be any unique
identifier.
pdbx_robot_system
The details about each robotic system used to collect data for this
project.
0
1
0
1
0
1
1
pdbx_robot_systemCategory
This property indicates that datablock
has a category element pdbx_robot_system.
pdbx_robot_systemItem
Abstract Datatype property for pdbx_robot_system items.
reference_to_pdbx_robot_system
cross-reference to pdbx_robot_system
pdbx_robot_system.manufacturer
The name of the manufacturer of the robotic system.
pdbx_robot_system.model
The model of the robotic system.
pdbx_robot_system.type
The type of robotic system used for in the production pathway.
pdbx_robot_system.id
Assign a numerical ID to each instrument.
pdbx_sequence_range
Data items in the PDBX_SEQUENCE_RANGE category identify the
beginning and ending points of polypeptide sequence segments.
Example 1 -
<PDBx:pdbx_sequence_rangeCategory>
<PDBx:pdbx_sequence_range beg_label_alt_id="A" beg_label_asym_id="A" beg_label_comp_id="PRO" beg_label_seq_id="1" end_label_alt_id="A" end_label_asym_id="A" end_label_comp_id="GLY" end_label_seq_id="29" seq_range_id="s1"></PDBx:pdbx_sequence_range>
<PDBx:pdbx_sequence_range beg_label_alt_id="A" beg_label_asym_id="D" beg_label_comp_id="PRO" beg_label_seq_id="91" end_label_alt_id="A" end_label_asym_id="D" end_label_comp_id="GLY" end_label_seq_id="119" seq_range_id="s2"></PDBx:pdbx_sequence_range>
</PDBx:pdbx_sequence_rangeCategory>
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
1
1
1
1
1
pdbx_sequence_rangeCategory
This property indicates that datablock
has a category element pdbx_sequence_range.
pdbx_sequence_rangeItem
Abstract Datatype property for pdbx_sequence_range items.
reference_to_pdbx_sequence_range
cross-reference to pdbx_sequence_range
pdbx_sequence_range.beg_auth_asym_id
A component of the identifier for the monomer at which this
segment of the sequence range begins.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_sequence_range.beg_auth_comp_id
A component of the identifier for the monomer at which this
segment of the sequence range begins.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_sequence_range.beg_auth_seq_id
A component of the identifier for the monomer at which this
segment of the sequence range begins.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_sequence_range.end_auth_asym_id
A component of the identifier for the monomer at which this
segment of the sequence range ends.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_sequence_range.end_auth_comp_id
A component of the identifier for the monomer at which this
segment of the sequence range ends.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_sequence_range.end_auth_seq_id
A component of the identifier for the monomer at which this
segment of the sequence range ends.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_sequence_range.beg_label_alt_id
A component of the identifier for the monomer at which this
segment of the sequence range begins.
This data item is a pointer to attribute id in category atom_sites_alt in the
ATOM_SITES_ALT category.
pdbx_sequence_range.beg_label_asym_id
A component of the identifier for the monomer at which this
segment of the sequence range begins.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_sequence_range.beg_label_comp_id
A component of the identifier for the monomer at which this
segment of the sequence range begins.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_sequence_range.beg_label_seq_id
A component of the identifier for the monomer at which this
segment of the sequence range begins.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_sequence_range.end_label_alt_id
A component of the identifier for the monomer at which this
segment of the sequence range ends.
This data item is a pointer to attribute id in category atom_sites_alt in the
ATOM_SITES_ALT category.
pdbx_sequence_range.end_label_asym_id
A component of the identifier for the monomer at which this
segment of the sequence range ends.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_sequence_range.end_label_comp_id
A component of the identifier for the monomer at which this
segment of the sequence range ends.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_sequence_range.end_label_seq_id
A component of the identifier for the monomer at which this
segment of the sequence range ends.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_sequence_range.seq_range_id
This data item is an identifier for a sequence range.
pdbx_soln_scatter
Data items in the PDBX_SOLN_SCATTER category record details about a
solution scattering experiment
Example 1 - based on PDB entry 1HAQ
<PDBx:pdbx_soln_scatterCategory>
<PDBx:pdbx_soln_scatter entry_id="1HAQ" id="1">
<PDBx:buffer_name>tris</PDBx:buffer_name>
<PDBx:concentration_range>0.7 - 14</PDBx:concentration_range>
<PDBx:detector_specific></PDBx:detector_specific>
<PDBx:detector_type>500-channel quadrant</PDBx:detector_type>
<PDBx:max_mean_cross_sectional_radii_gyration>1.7</PDBx:max_mean_cross_sectional_radii_gyration>
<PDBx:max_mean_cross_sectional_radii_gyration_esd>0.1</PDBx:max_mean_cross_sectional_radii_gyration_esd>
<PDBx:mean_guiner_radius>11.1</PDBx:mean_guiner_radius>
<PDBx:mean_guiner_radius_esd>0.4</PDBx:mean_guiner_radius_esd>
<PDBx:min_mean_cross_sectional_radii_gyration>4.4</PDBx:min_mean_cross_sectional_radii_gyration>
<PDBx:min_mean_cross_sectional_radii_gyration_esd>0.2</PDBx:min_mean_cross_sectional_radii_gyration_esd>
<PDBx:num_time_frames>10</PDBx:num_time_frames>
<PDBx:protein_length>40</PDBx:protein_length>
<PDBx:sample_pH></PDBx:sample_pH>
<PDBx:source_beamline>2.1</PDBx:source_beamline>
<PDBx:source_beamline_instrument></PDBx:source_beamline_instrument>
<PDBx:source_class>synchrotron</PDBx:source_class>
<PDBx:source_type>SRS BEAMLINE 2.1</PDBx:source_type>
<PDBx:temperature>288</PDBx:temperature>
<PDBx:type>x-ray</PDBx:type>
</PDBx:pdbx_soln_scatter>
<PDBx:pdbx_soln_scatter entry_id="1HAQ" id="2">
<PDBx:buffer_name>PBS in 99.9% D2O</PDBx:buffer_name>
<PDBx:concentration_range>0.4 - 9.6</PDBx:concentration_range>
<PDBx:detector_specific></PDBx:detector_specific>
<PDBx:detector_type>area</PDBx:detector_type>
<PDBx:max_mean_cross_sectional_radii_gyration>1.51</PDBx:max_mean_cross_sectional_radii_gyration>
<PDBx:max_mean_cross_sectional_radii_gyration_esd>0.06</PDBx:max_mean_cross_sectional_radii_gyration_esd>
<PDBx:mean_guiner_radius>11.3</PDBx:mean_guiner_radius>
<PDBx:mean_guiner_radius_esd>0.4</PDBx:mean_guiner_radius_esd>
<PDBx:min_mean_cross_sectional_radii_gyration>3.9</PDBx:min_mean_cross_sectional_radii_gyration>
<PDBx:min_mean_cross_sectional_radii_gyration_esd>0.2</PDBx:min_mean_cross_sectional_radii_gyration_esd>
<PDBx:num_time_frames></PDBx:num_time_frames>
<PDBx:protein_length>37.0 - 39.0</PDBx:protein_length>
<PDBx:sample_pH></PDBx:sample_pH>
<PDBx:source_beamline></PDBx:source_beamline>
<PDBx:source_beamline_instrument>D11, D22</PDBx:source_beamline_instrument>
<PDBx:source_class>neutron source</PDBx:source_class>
<PDBx:source_type>ILL</PDBx:source_type>
<PDBx:temperature></PDBx:temperature>
<PDBx:type>neutron</PDBx:type>
</PDBx:pdbx_soln_scatter>
<PDBx:pdbx_soln_scatter entry_id="1HAQ" id="3">
<PDBx:buffer_name>PBS in 99.9% D2O</PDBx:buffer_name>
<PDBx:concentration_range>3.7, 6.1</PDBx:concentration_range>
<PDBx:detector_specific></PDBx:detector_specific>
<PDBx:detector_type>AREA (TIME-OF-FLIGHT)</PDBx:detector_type>
<PDBx:max_mean_cross_sectional_radii_gyration></PDBx:max_mean_cross_sectional_radii_gyration>
<PDBx:max_mean_cross_sectional_radii_gyration_esd></PDBx:max_mean_cross_sectional_radii_gyration_esd>
<PDBx:mean_guiner_radius>11.7</PDBx:mean_guiner_radius>
<PDBx:mean_guiner_radius_esd>0.5</PDBx:mean_guiner_radius_esd>
<PDBx:min_mean_cross_sectional_radii_gyration></PDBx:min_mean_cross_sectional_radii_gyration>
<PDBx:min_mean_cross_sectional_radii_gyration_esd></PDBx:min_mean_cross_sectional_radii_gyration_esd>
<PDBx:num_time_frames></PDBx:num_time_frames>
<PDBx:protein_length>40.0</PDBx:protein_length>
<PDBx:sample_pH></PDBx:sample_pH>
<PDBx:source_beamline>Pulsed Neutron</PDBx:source_beamline>
<PDBx:source_beamline_instrument>LOQ</PDBx:source_beamline_instrument>
<PDBx:source_class>neutron source</PDBx:source_class>
<PDBx:source_type>ISIS</PDBx:source_type>
<PDBx:temperature></PDBx:temperature>
<PDBx:type>neutron</PDBx:type>
</PDBx:pdbx_soln_scatter>
</PDBx:pdbx_soln_scatterCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
pdbx_soln_scatterCategory
This property indicates that datablock
has a category element pdbx_soln_scatter.
pdbx_soln_scatterItem
Abstract Datatype property for pdbx_soln_scatter items.
reference_to_pdbx_soln_scatter
cross-reference to pdbx_soln_scatter
pdbx_soln_scatter.buffer_name
The name of the buffer used for the sample in the solution scattering
experiment.
acetic acid
pdbx_soln_scatter.concentration_range
The concentration range (mg/mL) of the complex in the
sample used in the solution scattering experiment to
determine the mean radius of structural elongation.
0.7 - 14
pdbx_soln_scatter.data_analysis_software_list
A list of the software used in the data analysis
SCTPL5 GNOM
pdbx_soln_scatter.data_reduction_software_list
A list of the software used in the data reduction
OTOKO
pdbx_soln_scatter.detector_specific
The particular radiation detector. In general this will be a
manufacturer, description, model number or some combination of
these.
pdbx_soln_scatter.detector_type
The general class of the radiation detector.
pdbx_soln_scatter.max_mean_cross_sectional_radii_gyration
The maximum mean radius of structural elongation of the sample.
In a given solute-solvent contrast, the radius of gyration
R_G is a measure of structural elongation if the internal
inhomogeneity of scattering densities has no effect. Guiner
analysis at low Q give the R_G and the forward scattering at
zero angle I(0).
lnl(Q) = lnl(0) - R_G^2Q^2/3
where
Q = 4(pi)sin(theta/lamda)
2theta = scattering angle
lamda = wavelength
The above expression is valid in a QR_G range for extended
rod-like particles. The relative I(0)/c values ( where
c = sample concentration) for sample measurements in a
constant buffer for a single sample data session, gives the
relative masses of the protein(s) studied when referenced
against a standard.
see:
O.Glatter & O.Kratky, (1982). Editors of "Small angle
X-ray Scattering, Academic Press, New York.
O.Kratky. (1963). X-ray small angle scattering with
substances of biological interest in diluted solutions.
Prog. Biophys. Chem., 13, 105-173.
G.D.Wignall & F.S.Bates, (1987). The small-angle approximation
of X-ray and neutron scatter from rigid rods of non-uniform
cross section and finite length. J.Appl. Crystallog., 18, 452-460.
If the structure is elongated, the mean radius of gyration
of the cross-sectional structure R_XS and the mean cross sectional
intensity at zero angle [I(Q).Q]_Q->0 is obtained from
ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2
pdbx_soln_scatter.max_mean_cross_sectional_radii_gyration_esd
The estimated standard deviation for the
minimum mean radius of structural elongation of the sample.
In a given solute-solvent contrast, the radius of gyration
R_G is a measure of structural elongation if the internal
inhomogeneity of scattering densities has no effect. Guiner
analysis at low Q give the R_G and the forward scattering at
zero angle I(0).
lnl(Q) = lnl(0) - R_G^2Q^2/3
where
Q = 4(pi)sin(theta/lamda)
2theta = scattering angle
lamda = wavelength
The above expression is valid in a QR_G range for extended
rod-like particles. The relative I(0)/c values ( where
c = sample concentration) for sample measurements in a
constant buffer for a single sample data session, gives the
relative masses of the protein(s) studied when referenced
against a standard.
see:
O.Glatter & O.Kratky, (1982). Editors of "Small angle
X-ray Scattering, Academic Press, New York.
O.Kratky. (1963). X-ray small angle scattering with
substances of biological interest in diluted solutions.
Prog. Biophys. Chem., 13, 105-173.
G.D.Wignall & F.S.Bates, (1987). The small-angle approximation
of X-ray and neutron scatter from rigid rods of non-uniform
cross section and finite length. J.Appl. Crystallog., 18, 452-460.
If the structure is elongated, the mean radius of gyration
of the cross-sectional structure R_XS and the mean cross sectional
intensity at zero angle [I(Q).Q]_Q->0 is obtained from
ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2
pdbx_soln_scatter.mean_guiner_radius
The mean radius of structural elongation of the sample.
In a given solute-solvent contrast, the radius of gyration
R_G is a measure of structural elongation if the internal
inhomogeneity of scattering densities has no effect. Guiner
analysis at low Q gives the R_G and the forward scattering at
zero angle I(0).
lnl(Q) = lnl(0) - R_G^2Q^2/3
where
Q = 4(pi)sin(theta/lamda)
2theta = scattering angle
lamda = wavelength
The above expression is valid in a QR_G range for extended
rod-like particles. The relative I(0)/c values ( where
c = sample concentration) for sample measurements in a
constant buffer for a single sample data session, gives the
relative masses of the protein(s) studied when referenced
against a standard.
see: O.Glatter & O.Kratky, (1982). Editors of "Small angle
X-ray Scattering, Academic Press, New York.
O.Kratky. (1963). X-ray small angle scattering with
substances of biological interest in diluted solutions.
Prog. Biophys. Chem., 13, 105-173.
G.D.Wignall & F.S.Bates, (1987). The small-angle approximation
of X-ray and neutron scatter from rigid rods of non-uniform
cross section and finite length. J.Appl. Crystallog., 18, 452-460.
If the structure is elongated, the mean radius of gyration
of the cross-sectional structure R_XS and the mean cross sectional
intensity at zero angle [I(Q).Q]_Q->0 is obtained from
ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2
pdbx_soln_scatter.mean_guiner_radius_esd
The estimated standard deviation for the
mean radius of structural elongation of the sample.
In a given solute-solvent contrast, the radius of gyration
R_G is a measure of structural elongation if the internal
inhomogeneity of scattering densities has no effect. Guiner
analysis at low Q give the R_G and the forward scattering at
zero angle I(0).
lnl(Q) = lnl(0) - R_G^2Q^2/3
where
Q = 4(pi)sin(theta/lamda)
2theta = scattering angle
lamda = wavelength
The above expression is valid in a QR_G range for extended
rod-like particles. The relative I(0)/c values ( where
c = sample concentration) for sample measurements in a
constant buffer for a single sample data session, gives the
relative masses of the protein(s) studied when referenced
against a standard.
see:
O.Glatter & O.Kratky, (1982). Editors of "Small angle
X-ray Scattering, Academic Press, New York.
O.Kratky. (1963). X-ray small angle scattering with
substances of biological interest in diluted solutions.
Prog. Biophys. Chem., 13, 105-173.
G.D.Wignall & F.S.Bates, (1987). The small-angle approximation
of X-ray and neutron scatter from rigid rods of non-uniform
cross section and finite length. J.Appl. Crystallog., 18, 452-460.
If the structure is elongated, the mean radius of gyration
of the cross-sectional structure R_XS and the mean cross sectional
intensity at zero angle [I(Q).Q]_Q->0 is obtained from
ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2
pdbx_soln_scatter.min_mean_cross_sectional_radii_gyration
The minimum mean radius of structural elongation of the sample.
In a given solute-solvent contrast, the radius of gyration
R_G is a measure of structural elongation if the internal
inhomogeneity of scattering densities has no effect. Guiner
analysis at low Q give the R_G and the forward scattering at
zero angle I(0).
lnl(Q) = lnl(0) - R_G^2Q^2/3
where
Q = 4(pi)sin(theta/lamda)
2theta = scattering angle
lamda = wavelength
The above expression is valid in a QR_G range for extended
rod-like particles. The relative I(0)/c values ( where
c = sample concentration) for sample measurements in a
constant buffer for a single sample data session, gives the
relative masses of the protein(s) studied when referenced
against a standard.
see:
O.Glatter & O.Kratky, (1982). Editors of "Small angle
X-ray Scattering, Academic Press, New York.
O.Kratky. (1963). X-ray small angle scattering with
substances of biological interest in diluted solutions.
Prog. Biophys. Chem., 13, 105-173.
G.D.Wignall & F.S.Bates, (1987). The small-angle approximation
of X-ray and neutron scatter from rigid rods of non-uniform
cross section and finite length. J.Appl. Crystallog., 18, 452-460.
If the structure is elongated, the mean radius of gyration
of the cross-sectional structure R_XS and the mean cross sectional
intensity at zero angle [I(Q).Q]_Q->0 is obtained from
ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2
pdbx_soln_scatter.min_mean_cross_sectional_radii_gyration_esd
The estimated standard deviation for the
minimum mean radius of structural elongation of the sample.
In a given solute-solvent contrast, the radius of gyration
R_G is a measure of structural elongation if the internal
inhomogeneity of scattering densities has no effect. Guiner
analysis at low Q give the R_G and the forward scattering at
zero angle I(0).
lnl(Q) = lnl(0) - R_G^2Q^2/3
where
Q = 4(pi)sin(theta/lamda)
2theta = scattering angle
lamda = wavelength
The above expression is valid in a QR_G range for extended
rod-like particles. The relative I(0)/c values ( where
c = sample concentration) for sample measurements in a
constant buffer for a single sample data session, gives the
relative masses of the protein(s) studied when referenced
against a standard.
see:
O.Glatter & O.Kratky, (1982). Editors of "Small angle
X-ray Scattering, Academic Press, New York.
O.Kratky. (1963). X-ray small angle scattering with
substances of biological interest in diluted solutions.
Prog. Biophys. Chem., 13, 105-173.
G.D.Wignall & F.S.Bates, (1987). The small-angle approximation
of X-ray and neutron scatter from rigid rods of non-uniform
cross section and finite length. J.Appl. Crystallog., 18, 452-460.
If the structure is elongated, the mean radius of gyration
of the cross-sectional structure R_XS and the mean cross sectional
intensity at zero angle [I(Q).Q]_Q->0 is obtained from
ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2
pdbx_soln_scatter.num_time_frames
The number of time frame solution scattering images used.
pdbx_soln_scatter.protein_length
The length (or range) of the protein sample under study.
If the solution structure is approximated as an elongated elliptical
cyclinder the the length L is determined from,
L = sqrt [12( (R_G)^2 - (R_XS)^2 ) ]
The length should also be given by
L = pi I(0) / [ I(Q).Q]_Q->0
pdbx_soln_scatter.sample_pH
The pH value of the buffered sample.
pdbx_soln_scatter.source_beamline
The beamline name used for the experiment
pdbx_soln_scatter.source_beamline_instrument
The instrumentation used on the beamline
pdbx_soln_scatter.source_class
The general class of the radiation source.
neutron source
synchrotron
pdbx_soln_scatter.source_type
The make, model, name or beamline of the source of radiation.
pdbx_soln_scatter.temperature
The temperature in kelvins at which the experiment
was conducted
x-ray
neutron
modelling
The type of solution scattering experiment carried out
pdbx_soln_scatter.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
pdbx_soln_scatter.id
The value of attribute id in category pdbx_soln_scatter must
uniquely identify the sample in the category PDBX_SOLN_SCATTER
pdbx_soln_scatter_model
Data items in the PDBX_SOLN_SCATTER_MODEL category record details about the
homology model fitting to the solution scatter data.
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
pdbx_soln_scatter_modelCategory
This property indicates that datablock
has a category element pdbx_soln_scatter_model.
pdbx_soln_scatter_modelItem
Abstract Datatype property for pdbx_soln_scatter_model items.
reference_to_pdbx_soln_scatter_model
cross-reference to pdbx_soln_scatter_model
pdbx_soln_scatter_model.conformer_selection_criteria
A description of the conformer selection criteria
used.
The modelled scattering curves were assessed by calculation of the
RG, RSX-1 and RXS-2 values in the same Q ranges
used in the experimental Guinier fits. models were
then ranked using a goodness-of-fit R-factor
defined by analogy with protein crystallography
and based on the experimental curves in the Q range
extending to 1.4 nm-1.
pdbx_soln_scatter_model.details
A description of any additional details concerning the experiment.
Homology models were built for
the 17 SCR domains and energy minimisations were
performed to improve the connectivity in the fh model.
triantennary complex-type carbohydrate structures
(MAN3GLCNAC6GAL3FUC3NEUNAC1) were added to each of the
N-linked glycosylation sites. a library of linker peptide
conformations was used in domain modelling constrained
by the solution scattering fits. modelling with the
scattering data was also carried out by rotational
search methods. the x-ray and neutron scattering curve
I(Q) was calculated assuming a uniform scattering density
for the spheres using the debye equation as adapted to
spheres. x-ray curves were calculated from the hydrated
sphere models without corrections for wavelength spread or
beam divergence, while these corrections were applied for
the neutron curves but now using unhydrated models.
pdbx_soln_scatter_model.entry_fitting_list
A list of the entries used to fit the model
to the scattering data
PDB CODE 1HFI, 1HCC, 1HFH, 1VCC
pdbx_soln_scatter_model.method
A description of the methods used in the modelling
Constrained scattering fitting of homology models
pdbx_soln_scatter_model.num_conformers_calculated
The number of model conformers calculated.
pdbx_soln_scatter_model.num_conformers_submitted
The number of model conformers submitted in the entry
pdbx_soln_scatter_model.representative_conformer
The index of the representative conformer among the submitted conformers for the entry
pdbx_soln_scatter_model.software_author_list
A list of the software authors
MSI
pdbx_soln_scatter_model.software_list
A list of the software used in the modeeling
INSIGHT II, HOMOLOGY, DISCOVERY, BIOPOLYMER, DELPHI
pdbx_soln_scatter_model.id
The value of attribute id in category pdbx_soln_scatter_model must
uniquely identify the sample in the category PDBX_SOLN_SCATTER_MODEL
pdbx_soln_scatter_model.scatter_id
This data item is a pointer to attribute id in category pdbx_soln_scatter in the PDBX_SOLN_SCATTER category.
pdbx_struct_assembly
Data items in the PDBX_STRUCT_ASSEMBLY category record details about
the structural elements that form macromolecular assemblies.
Example 1 -
<PDBx:pdbx_struct_assemblyCategory>
<PDBx:pdbx_struct_assembly id="1">
<PDBx:details> The icosahedral virus particle.</PDBx:details>
</PDBx:pdbx_struct_assembly>
</PDBx:pdbx_struct_assemblyCategory>
0
1
0
1
0
1
0
1
1
pdbx_struct_assemblyCategory
This property indicates that datablock
has a category element pdbx_struct_assembly.
pdbx_struct_assemblyItem
Abstract Datatype property for pdbx_struct_assembly items.
reference_to_pdbx_struct_assembly
cross-reference to pdbx_struct_assembly
pdbx_struct_assembly.details
A description of special aspects of the macromolecular assembly.
The icosahedral virus particle.
pdbx_struct_assembly.method_details
Provides details of the method used to determine or
compute the assembly.
pdbx_struct_assembly.oligomeric_count
The number of polymer molecules in the assembly.
pdbx_struct_assembly.oligomeric_details
Provides the details of the oligomeric state of the assembly.
monomer
octameric
tetradecameric
eicosameric
21-meric
60-meric
180-meric
helical
pdbx_struct_assembly.id
The value of attribute id in category pdbx_struct_assembly must uniquely identify a record in
the PDBX_STRUCT_ASSEMBLY list.
pdbx_struct_assembly_gen
Data items in the PDBX_STRUCT_ASSEMBLY_GEN category record details about
the generation of each macromolecular assemblies. The PDBX_STRUCT_ASSEMBLY_GEN
data items provide the specifications of the components that
constitute that assembly in terms of cartesian transformations.
Example 1 -
<PDBx:pdbx_struct_assembly_genCategory>
<PDBx:pdbx_struct_assembly_gen assembly_id="1" asym_id_list="A" oper_expression="1"></PDBx:pdbx_struct_assembly_gen>
<PDBx:pdbx_struct_assembly_gen assembly_id="1" asym_id_list="B" oper_expression="1"></PDBx:pdbx_struct_assembly_gen>
<PDBx:pdbx_struct_assembly_gen assembly_id="2" asym_id_list="A" oper_expression="2"></PDBx:pdbx_struct_assembly_gen>
<PDBx:pdbx_struct_assembly_gen assembly_id="2" asym_id_list="B" oper_expression="2"></PDBx:pdbx_struct_assembly_gen>
<PDBx:pdbx_struct_assembly_gen assembly_id="2" asym_id_list="C" oper_expression="2"></PDBx:pdbx_struct_assembly_gen>
<PDBx:pdbx_struct_assembly_gen assembly_id="3" asym_id_list="A" oper_expression="3"></PDBx:pdbx_struct_assembly_gen>
<PDBx:pdbx_struct_assembly_gen assembly_id="3" asym_id_list="B" oper_expression="3"></PDBx:pdbx_struct_assembly_gen>
<PDBx:pdbx_struct_assembly_gen assembly_id="3" asym_id_list="D" oper_expression="3"></PDBx:pdbx_struct_assembly_gen>
</PDBx:pdbx_struct_assembly_genCategory>
Example 2 -
<PDBx:pdbx_struct_assembly_genCategory>
<PDBx:pdbx_struct_assembly_gen assembly_id="1" asym_id_list="A,B" oper_expression="1"></PDBx:pdbx_struct_assembly_gen>
<PDBx:pdbx_struct_assembly_gen assembly_id="2" asym_id_list="A,B,C" oper_expression="2"></PDBx:pdbx_struct_assembly_gen>
<PDBx:pdbx_struct_assembly_gen assembly_id="3" asym_id_list="A,B,D" oper_expression="3"></PDBx:pdbx_struct_assembly_gen>
</PDBx:pdbx_struct_assembly_genCategory>
0
1
0
1
1
1
1
pdbx_struct_assembly_genCategory
This property indicates that datablock
has a category element pdbx_struct_assembly_gen.
pdbx_struct_assembly_genItem
Abstract Datatype property for pdbx_struct_assembly_gen items.
reference_to_pdbx_struct_assembly_gen
cross-reference to pdbx_struct_assembly_gen
pdbx_struct_assembly_gen.auth_asym_id_list
This data item is a pointer to attribute auth_asym_id in category atom_site in
the ATOM_SITE category.
This item may be expressed as a comma separated list of identifiers.
pdbx_struct_assembly_gen.entity_inst_id
This data item is a pointer to attribute id in category pdbx_struct_entity_inst in
the PDBX_STRUCT_ENTITY_INST category.
This item may be expressed as a comma separated list of instance identifiers.
pdbx_struct_assembly_gen.assembly_id
This data item is a pointer to attribute id in category pdbx_struct_assembly in the
PDBX_STRUCT_ASSEMBLY category.
pdbx_struct_assembly_gen.asym_id_list
This data item is a pointer to attribute id in category struct_asym in
the STRUCT_ASYM category.
This item may be expressed as a comma separated list of identifiers.
pdbx_struct_assembly_gen.oper_expression
Identifies the operation of collection of operations
from category PDBX_STRUCT_OPER_LIST.
Operation expressions may have the forms:
(1) the single operation 1
(1,2,5) the operations 1, 2, 5
(1-4) the operations 1,2,3 and 4
(1,2)(3,4) the combinations of operations
3 and 4 followed by 1 and 2 (i.e.
the cartesian product of parenthetical
groups applied from right to left)
(1)
(1,2,5)
(1-60)
(1-60)(61)
pdbx_struct_assembly_prop
Properties and features of structural assemblies.
Example 1 -
<PDBx:pdbx_struct_assembly_propCategory>
<PDBx:pdbx_struct_assembly_prop biol_id="1" type="ABSA">
<PDBx:details> </PDBx:details>
<PDBx:value>1456.7</PDBx:value>
</PDBx:pdbx_struct_assembly_prop>
</PDBx:pdbx_struct_assembly_propCategory>
0
1
1
1
1
1
pdbx_struct_assembly_propCategory
This property indicates that datablock
has a category element pdbx_struct_assembly_prop.
pdbx_struct_assembly_propItem
Abstract Datatype property for pdbx_struct_assembly_prop items.
reference_to_pdbx_struct_assembly_prop
cross-reference to pdbx_struct_assembly_prop
pdbx_struct_assembly_prop.details
Additional details about this assembly property.
pdbx_struct_assembly_prop.value
The value of the assembly property.
pdbx_struct_assembly_prop.biol_id
The identifier for the assembly used in category STRUCT_BIOL.
ABSA (A^2)
SSA (A^2)
MORE
The property type for the assembly.
pdbx_struct_asym_gen
Data items in the PDBX_STRUCT_ASYM_GEN category record details about
the generation of the crystallographic asymmetric unit. The
PDBX_STRUCT_ASYM_GEN data items provide the specifications of the
components that constitute the asymmetric unit in terms of cartesian
transformations of deposited coordinates.
Example 1 -
<PDBx:pdbx_struct_asym_genCategory>
<PDBx:pdbx_struct_asym_gen entity_inst_id="A" oper_expression="1">
<PDBx:asym_id>A</PDBx:asym_id>
</PDBx:pdbx_struct_asym_gen>
<PDBx:pdbx_struct_asym_gen entity_inst_id="B" oper_expression="1">
<PDBx:asym_id>B</PDBx:asym_id>
</PDBx:pdbx_struct_asym_gen>
</PDBx:pdbx_struct_asym_genCategory>
0
1
1
1
pdbx_struct_asym_genCategory
This property indicates that datablock
has a category element pdbx_struct_asym_gen.
pdbx_struct_asym_genItem
Abstract Datatype property for pdbx_struct_asym_gen items.
reference_to_pdbx_struct_asym_gen
cross-reference to pdbx_struct_asym_gen
pdbx_struct_asym_gen.asym_id
This data item is a pointer to attribute id in category struct_asym in the
STRUCT_ASYM category.
pdbx_struct_asym_gen.entity_inst_id
This data item is a pointer to attribute id in category pdbx_struct_entity_inst in
the PDBX_STRUCT_ENTITY_INST category.
pdbx_struct_asym_gen.oper_expression
Identifies the operation from category PDBX_STRUCT_OPER_LIST.
(1)
(1-2)
pdbx_struct_chem_comp_diagnostics
Data items in the PDBX_STRUCT_CHEM_COMP_DIAGNOSTICS category provides
structural diagnostics in chemical components instances.
Example 1 -
<PDBx:pdbx_struct_chem_comp_diagnosticsCategory>
<PDBx:pdbx_struct_chem_comp_diagnostics ordinal="1">
<PDBx:asym_id>Q</PDBx:asym_id>
<PDBx:auth_comp_id>Q20</PDBx:auth_comp_id>
<PDBx:auth_seq_id>10</PDBx:auth_seq_id>
<PDBx:details>Strained geometry. Long carbonyl bond at C10.</PDBx:details>
<PDBx:pdb_strand_id>Q</PDBx:pdb_strand_id>
<PDBx:seq_num></PDBx:seq_num>
<PDBx:type>GEOMETRY</PDBx:type>
</PDBx:pdbx_struct_chem_comp_diagnostics>
</PDBx:pdbx_struct_chem_comp_diagnosticsCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
pdbx_struct_chem_comp_diagnosticsCategory
This property indicates that datablock
has a category element pdbx_struct_chem_comp_diagnostics.
pdbx_struct_chem_comp_diagnosticsItem
Abstract Datatype property for pdbx_struct_chem_comp_diagnostics items.
reference_to_pdbx_struct_chem_comp_diagnostics
cross-reference to pdbx_struct_chem_comp_diagnostics
pdbx_struct_chem_comp_diagnostics.asym_id
Instance identifier for the polymer molecule.
A
B
pdbx_struct_chem_comp_diagnostics.auth_comp_id
PDB component ID
NAG
ATP
pdbx_struct_chem_comp_diagnostics.auth_seq_id
PDB position in the sequence.
1
2
pdbx_struct_chem_comp_diagnostics.details
Special structural details about this chemical component.
pdbx_struct_chem_comp_diagnostics.pdb_ins_code
Insertion code of the monomer or ligand .
A
B
pdbx_struct_chem_comp_diagnostics.pdb_strand_id
PDB strand/chain id.
A
B
pdbx_struct_chem_comp_diagnostics.seq_num
Position in the sequence.
1
2
MISSING_ATOM
STEREOCHEMISTRY
VALENCE
GEOMETRY
LABELING
OTHER
A classification of the diagnostic for the chemical
component instance
pdbx_struct_chem_comp_diagnostics.ordinal
An ordinal index for this category
1
2
pdbx_struct_chem_comp_feature
Data items in the PDBX_STRUCT_CHEM_COMP_FEATURE category provides
structural annotations in chemical components instances.
Example 1 -
<PDBx:pdbx_struct_chem_comp_featureCategory>
<PDBx:pdbx_struct_chem_comp_feature ordinal="1">
<PDBx:asym_id>Q</PDBx:asym_id>
<PDBx:auth_comp_id>Q20</PDBx:auth_comp_id>
<PDBx:auth_seq_id>10</PDBx:auth_seq_id>
<PDBx:details>Helix of length 4 beginning at atom position C2A.</PDBx:details>
<PDBx:pdb_strand_id>Q</PDBx:pdb_strand_id>
<PDBx:seq_num></PDBx:seq_num>
<PDBx:type>SECONDARY STRUCTURE</PDBx:type>
</PDBx:pdbx_struct_chem_comp_feature>
</PDBx:pdbx_struct_chem_comp_featureCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
pdbx_struct_chem_comp_featureCategory
This property indicates that datablock
has a category element pdbx_struct_chem_comp_feature.
pdbx_struct_chem_comp_featureItem
Abstract Datatype property for pdbx_struct_chem_comp_feature items.
reference_to_pdbx_struct_chem_comp_feature
cross-reference to pdbx_struct_chem_comp_feature
pdbx_struct_chem_comp_feature.asym_id
Instance identifier for the polymer molecule.
A
B
pdbx_struct_chem_comp_feature.auth_comp_id
PDB component ID
NAG
ATP
pdbx_struct_chem_comp_feature.auth_seq_id
PDB position in the sequence.
1
2
pdbx_struct_chem_comp_feature.details
Special structural details about this chemical component.
pdbx_struct_chem_comp_feature.pdb_ins_code
Insertion code of the monomer or ligand .
A
B
pdbx_struct_chem_comp_feature.pdb_strand_id
PDB strand/chain id.
A
B
pdbx_struct_chem_comp_feature.seq_num
Position in the sequence.
1
2
SECONDARY STRUCTURE
STEREOCHEMISTRY
GEOMETRY
OTHER
A classification of the annotation for the chemical
component instance
pdbx_struct_chem_comp_feature.ordinal
An ordinal index for this category
1
2
pdbx_struct_conn_angle
Data items in the PDBX_STRUCT_CONN_ANGLE category record the angles
in connections between portions of the structure.
Example 1 PDB entry 2v8d
<PDBx:pdbx_struct_conn_angleCategory>
<PDBx:pdbx_struct_conn_angle id="1">
<PDBx:ptnr1_PDB_ins_code></PDBx:ptnr1_PDB_ins_code>
<PDBx:ptnr1_label_asym_id>A</PDBx:ptnr1_label_asym_id>
<PDBx:ptnr1_label_atom_id>OD</PDBx:ptnr1_label_atom_id>
<PDBx:ptnr1_label_comp_id>ASP</PDBx:ptnr1_label_comp_id>
<PDBx:ptnr1_label_seq_id>125</PDBx:ptnr1_label_seq_id>
<PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code>
<PDBx:ptnr2_label_asym_id>A</PDBx:ptnr2_label_asym_id>
<PDBx:ptnr2_label_atom_id></PDBx:ptnr2_label_atom_id>
<PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id>
<PDBx:ptnr2_label_seq_id>500</PDBx:ptnr2_label_seq_id>
<PDBx:ptnr3_PDB_ins_code>NE</PDBx:ptnr3_PDB_ins_code>
<PDBx:ptnr3_label_asym_id>A</PDBx:ptnr3_label_asym_id>
<PDBx:ptnr3_label_atom_id></PDBx:ptnr3_label_atom_id>
<PDBx:ptnr3_label_comp_id>HIS</PDBx:ptnr3_label_comp_id>
<PDBx:ptnr3_label_seq_id>114</PDBx:ptnr3_label_seq_id>
<PDBx:value>104.7</PDBx:value>
</PDBx:pdbx_struct_conn_angle>
<PDBx:pdbx_struct_conn_angle id="2">
<PDBx:ptnr1_PDB_ins_code></PDBx:ptnr1_PDB_ins_code>
<PDBx:ptnr1_label_asym_id>A</PDBx:ptnr1_label_asym_id>
<PDBx:ptnr1_label_atom_id>OD</PDBx:ptnr1_label_atom_id>
<PDBx:ptnr1_label_comp_id>ASP</PDBx:ptnr1_label_comp_id>
<PDBx:ptnr1_label_seq_id>125</PDBx:ptnr1_label_seq_id>
<PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code>
<PDBx:ptnr2_label_asym_id>A</PDBx:ptnr2_label_asym_id>
<PDBx:ptnr2_label_atom_id></PDBx:ptnr2_label_atom_id>
<PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id>
<PDBx:ptnr2_label_seq_id>500</PDBx:ptnr2_label_seq_id>
<PDBx:ptnr3_PDB_ins_code>NE</PDBx:ptnr3_PDB_ins_code>
<PDBx:ptnr3_label_asym_id>A</PDBx:ptnr3_label_asym_id>
<PDBx:ptnr3_label_atom_id></PDBx:ptnr3_label_atom_id>
<PDBx:ptnr3_label_comp_id>HIS</PDBx:ptnr3_label_comp_id>
<PDBx:ptnr3_label_seq_id>226</PDBx:ptnr3_label_seq_id>
<PDBx:value>91.3</PDBx:value>
</PDBx:pdbx_struct_conn_angle>
<PDBx:pdbx_struct_conn_angle id="3">
<PDBx:ptnr1_PDB_ins_code></PDBx:ptnr1_PDB_ins_code>
<PDBx:ptnr1_label_asym_id>A</PDBx:ptnr1_label_asym_id>
<PDBx:ptnr1_label_atom_id>NE</PDBx:ptnr1_label_atom_id>
<PDBx:ptnr1_label_comp_id>HIS</PDBx:ptnr1_label_comp_id>
<PDBx:ptnr1_label_seq_id>114</PDBx:ptnr1_label_seq_id>
<PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code>
<PDBx:ptnr2_label_asym_id>A</PDBx:ptnr2_label_asym_id>
<PDBx:ptnr2_label_atom_id></PDBx:ptnr2_label_atom_id>
<PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id>
<PDBx:ptnr2_label_seq_id>500</PDBx:ptnr2_label_seq_id>
<PDBx:ptnr3_PDB_ins_code>NE</PDBx:ptnr3_PDB_ins_code>
<PDBx:ptnr3_label_asym_id>A</PDBx:ptnr3_label_asym_id>
<PDBx:ptnr3_label_atom_id></PDBx:ptnr3_label_atom_id>
<PDBx:ptnr3_label_comp_id>HIS</PDBx:ptnr3_label_comp_id>
<PDBx:ptnr3_label_seq_id>226</PDBx:ptnr3_label_seq_id>
<PDBx:value>120.6</PDBx:value>
</PDBx:pdbx_struct_conn_angle>
<PDBx:pdbx_struct_conn_angle id="4">
<PDBx:ptnr1_PDB_ins_code></PDBx:ptnr1_PDB_ins_code>
<PDBx:ptnr1_label_asym_id>A</PDBx:ptnr1_label_asym_id>
<PDBx:ptnr1_label_atom_id>OD</PDBx:ptnr1_label_atom_id>
<PDBx:ptnr1_label_comp_id>ASP</PDBx:ptnr1_label_comp_id>
<PDBx:ptnr1_label_seq_id>125</PDBx:ptnr1_label_seq_id>
<PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code>
<PDBx:ptnr2_label_asym_id>A</PDBx:ptnr2_label_asym_id>
<PDBx:ptnr2_label_atom_id></PDBx:ptnr2_label_atom_id>
<PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id>
<PDBx:ptnr2_label_seq_id>500</PDBx:ptnr2_label_seq_id>
<PDBx:ptnr3_PDB_ins_code>O</PDBx:ptnr3_PDB_ins_code>
<PDBx:ptnr3_label_asym_id>A</PDBx:ptnr3_label_asym_id>
<PDBx:ptnr3_label_atom_id></PDBx:ptnr3_label_atom_id>
<PDBx:ptnr3_label_comp_id>HOH</PDBx:ptnr3_label_comp_id>
<PDBx:ptnr3_label_seq_id>2041</PDBx:ptnr3_label_seq_id>
<PDBx:value>172.5</PDBx:value>
</PDBx:pdbx_struct_conn_angle>
<PDBx:pdbx_struct_conn_angle id="5">
<PDBx:ptnr1_PDB_ins_code></PDBx:ptnr1_PDB_ins_code>
<PDBx:ptnr1_label_asym_id>A</PDBx:ptnr1_label_asym_id>
<PDBx:ptnr1_label_atom_id>NE</PDBx:ptnr1_label_atom_id>
<PDBx:ptnr1_label_comp_id>HIS</PDBx:ptnr1_label_comp_id>
<PDBx:ptnr1_label_seq_id>114</PDBx:ptnr1_label_seq_id>
<PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code>
<PDBx:ptnr2_label_asym_id>A</PDBx:ptnr2_label_asym_id>
<PDBx:ptnr2_label_atom_id></PDBx:ptnr2_label_atom_id>
<PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id>
<PDBx:ptnr2_label_seq_id>500</PDBx:ptnr2_label_seq_id>
<PDBx:ptnr3_PDB_ins_code>O</PDBx:ptnr3_PDB_ins_code>
<PDBx:ptnr3_label_asym_id>A</PDBx:ptnr3_label_asym_id>
<PDBx:ptnr3_label_atom_id></PDBx:ptnr3_label_atom_id>
<PDBx:ptnr3_label_comp_id>HOH</PDBx:ptnr3_label_comp_id>
<PDBx:ptnr3_label_seq_id>2041</PDBx:ptnr3_label_seq_id>
<PDBx:value>80.0</PDBx:value>
</PDBx:pdbx_struct_conn_angle>
<PDBx:pdbx_struct_conn_angle id="6">
<PDBx:ptnr1_PDB_ins_code></PDBx:ptnr1_PDB_ins_code>
<PDBx:ptnr1_label_asym_id>A</PDBx:ptnr1_label_asym_id>
<PDBx:ptnr1_label_atom_id>NE</PDBx:ptnr1_label_atom_id>
<PDBx:ptnr1_label_comp_id>HIS</PDBx:ptnr1_label_comp_id>
<PDBx:ptnr1_label_seq_id>226</PDBx:ptnr1_label_seq_id>
<PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code>
<PDBx:ptnr2_label_asym_id>A</PDBx:ptnr2_label_asym_id>
<PDBx:ptnr2_label_atom_id></PDBx:ptnr2_label_atom_id>
<PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id>
<PDBx:ptnr2_label_seq_id>500</PDBx:ptnr2_label_seq_id>
<PDBx:ptnr3_PDB_ins_code>O</PDBx:ptnr3_PDB_ins_code>
<PDBx:ptnr3_label_asym_id>A</PDBx:ptnr3_label_asym_id>
<PDBx:ptnr3_label_atom_id></PDBx:ptnr3_label_atom_id>
<PDBx:ptnr3_label_comp_id>HOH</PDBx:ptnr3_label_comp_id>
<PDBx:ptnr3_label_seq_id>2041</PDBx:ptnr3_label_seq_id>
<PDBx:value>91.3</PDBx:value>
</PDBx:pdbx_struct_conn_angle>
<PDBx:pdbx_struct_conn_angle id="7">
<PDBx:ptnr1_PDB_ins_code></PDBx:ptnr1_PDB_ins_code>
<PDBx:ptnr1_label_asym_id>A</PDBx:ptnr1_label_asym_id>
<PDBx:ptnr1_label_atom_id>OD</PDBx:ptnr1_label_atom_id>
<PDBx:ptnr1_label_comp_id>ASP</PDBx:ptnr1_label_comp_id>
<PDBx:ptnr1_label_seq_id>125</PDBx:ptnr1_label_seq_id>
<PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code>
<PDBx:ptnr2_label_asym_id>A</PDBx:ptnr2_label_asym_id>
<PDBx:ptnr2_label_atom_id></PDBx:ptnr2_label_atom_id>
<PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id>
<PDBx:ptnr2_label_seq_id>500</PDBx:ptnr2_label_seq_id>
<PDBx:ptnr3_PDB_ins_code>O</PDBx:ptnr3_PDB_ins_code>
<PDBx:ptnr3_label_asym_id>A</PDBx:ptnr3_label_asym_id>
<PDBx:ptnr3_label_atom_id></PDBx:ptnr3_label_atom_id>
<PDBx:ptnr3_label_comp_id>HOH</PDBx:ptnr3_label_comp_id>
<PDBx:ptnr3_label_seq_id>3001</PDBx:ptnr3_label_seq_id>
<PDBx:value>76.9</PDBx:value>
</PDBx:pdbx_struct_conn_angle>
<PDBx:pdbx_struct_conn_angle id="8">
<PDBx:ptnr1_PDB_ins_code></PDBx:ptnr1_PDB_ins_code>
<PDBx:ptnr1_label_asym_id>A</PDBx:ptnr1_label_asym_id>
<PDBx:ptnr1_label_atom_id>NE</PDBx:ptnr1_label_atom_id>
<PDBx:ptnr1_label_comp_id>HIS</PDBx:ptnr1_label_comp_id>
<PDBx:ptnr1_label_seq_id>114</PDBx:ptnr1_label_seq_id>
<PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code>
<PDBx:ptnr2_label_asym_id>A</PDBx:ptnr2_label_asym_id>
<PDBx:ptnr2_label_atom_id></PDBx:ptnr2_label_atom_id>
<PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id>
<PDBx:ptnr2_label_seq_id>500</PDBx:ptnr2_label_seq_id>
<PDBx:ptnr3_PDB_ins_code>O</PDBx:ptnr3_PDB_ins_code>
<PDBx:ptnr3_label_asym_id>A</PDBx:ptnr3_label_asym_id>
<PDBx:ptnr3_label_atom_id></PDBx:ptnr3_label_atom_id>
<PDBx:ptnr3_label_comp_id>HOH</PDBx:ptnr3_label_comp_id>
<PDBx:ptnr3_label_seq_id>3001</PDBx:ptnr3_label_seq_id>
<PDBx:value>112.3</PDBx:value>
</PDBx:pdbx_struct_conn_angle>
<PDBx:pdbx_struct_conn_angle id="9">
<PDBx:ptnr1_PDB_ins_code></PDBx:ptnr1_PDB_ins_code>
<PDBx:ptnr1_label_asym_id>A</PDBx:ptnr1_label_asym_id>
<PDBx:ptnr1_label_atom_id>NE</PDBx:ptnr1_label_atom_id>
<PDBx:ptnr1_label_comp_id>HIS</PDBx:ptnr1_label_comp_id>
<PDBx:ptnr1_label_seq_id>226</PDBx:ptnr1_label_seq_id>
<PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code>
<PDBx:ptnr2_label_asym_id>A</PDBx:ptnr2_label_asym_id>
<PDBx:ptnr2_label_atom_id></PDBx:ptnr2_label_atom_id>
<PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id>
<PDBx:ptnr2_label_seq_id>500</PDBx:ptnr2_label_seq_id>
<PDBx:ptnr3_PDB_ins_code>O</PDBx:ptnr3_PDB_ins_code>
<PDBx:ptnr3_label_asym_id>A</PDBx:ptnr3_label_asym_id>
<PDBx:ptnr3_label_atom_id></PDBx:ptnr3_label_atom_id>
<PDBx:ptnr3_label_comp_id>HOH</PDBx:ptnr3_label_comp_id>
<PDBx:ptnr3_label_seq_id>3001</PDBx:ptnr3_label_seq_id>
<PDBx:value>127.0</PDBx:value>
</PDBx:pdbx_struct_conn_angle>
<PDBx:pdbx_struct_conn_angle id="10">
<PDBx:ptnr1_PDB_ins_code></PDBx:ptnr1_PDB_ins_code>
<PDBx:ptnr1_label_asym_id>A</PDBx:ptnr1_label_asym_id>
<PDBx:ptnr1_label_atom_id>O</PDBx:ptnr1_label_atom_id>
<PDBx:ptnr1_label_comp_id>HOH</PDBx:ptnr1_label_comp_id>
<PDBx:ptnr1_label_seq_id>2041</PDBx:ptnr1_label_seq_id>
<PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code>
<PDBx:ptnr2_label_asym_id>A</PDBx:ptnr2_label_asym_id>
<PDBx:ptnr2_label_atom_id></PDBx:ptnr2_label_atom_id>
<PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id>
<PDBx:ptnr2_label_seq_id>500</PDBx:ptnr2_label_seq_id>
<PDBx:ptnr3_PDB_ins_code>O</PDBx:ptnr3_PDB_ins_code>
<PDBx:ptnr3_label_asym_id>A</PDBx:ptnr3_label_asym_id>
<PDBx:ptnr3_label_atom_id></PDBx:ptnr3_label_atom_id>
<PDBx:ptnr3_label_comp_id>HOH</PDBx:ptnr3_label_comp_id>
<PDBx:ptnr3_label_seq_id>3001</PDBx:ptnr3_label_seq_id>
<PDBx:value>95.9</PDBx:value>
</PDBx:pdbx_struct_conn_angle>
<PDBx:pdbx_struct_conn_angle id="11">
<PDBx:ptnr1_PDB_ins_code></PDBx:ptnr1_PDB_ins_code>
<PDBx:ptnr1_label_asym_id>A</PDBx:ptnr1_label_asym_id>
<PDBx:ptnr1_label_atom_id>OD</PDBx:ptnr1_label_atom_id>
<PDBx:ptnr1_label_comp_id>ASP</PDBx:ptnr1_label_comp_id>
<PDBx:ptnr1_label_seq_id>125</PDBx:ptnr1_label_seq_id>
<PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code>
<PDBx:ptnr2_label_asym_id>A</PDBx:ptnr2_label_asym_id>
<PDBx:ptnr2_label_atom_id></PDBx:ptnr2_label_atom_id>
<PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id>
<PDBx:ptnr2_label_seq_id>501</PDBx:ptnr2_label_seq_id>
<PDBx:ptnr3_PDB_ins_code>OE</PDBx:ptnr3_PDB_ins_code>
<PDBx:ptnr3_label_asym_id>A</PDBx:ptnr3_label_asym_id>
<PDBx:ptnr3_label_atom_id></PDBx:ptnr3_label_atom_id>
<PDBx:ptnr3_label_comp_id>GLU</PDBx:ptnr3_label_comp_id>
<PDBx:ptnr3_label_seq_id>160</PDBx:ptnr3_label_seq_id>
<PDBx:value>89.8</PDBx:value>
</PDBx:pdbx_struct_conn_angle>
<PDBx:pdbx_struct_conn_angle id="12">
<PDBx:ptnr1_PDB_ins_code></PDBx:ptnr1_PDB_ins_code>
<PDBx:ptnr1_label_asym_id>A</PDBx:ptnr1_label_asym_id>
<PDBx:ptnr1_label_atom_id>OD</PDBx:ptnr1_label_atom_id>
<PDBx:ptnr1_label_comp_id>ASP</PDBx:ptnr1_label_comp_id>
<PDBx:ptnr1_label_seq_id>125</PDBx:ptnr1_label_seq_id>
<PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code>
<PDBx:ptnr2_label_asym_id>A</PDBx:ptnr2_label_asym_id>
<PDBx:ptnr2_label_atom_id></PDBx:ptnr2_label_atom_id>
<PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id>
<PDBx:ptnr2_label_seq_id>501</PDBx:ptnr2_label_seq_id>
<PDBx:ptnr3_PDB_ins_code>O</PDBx:ptnr3_PDB_ins_code>
<PDBx:ptnr3_label_asym_id>A</PDBx:ptnr3_label_asym_id>
<PDBx:ptnr3_label_atom_id></PDBx:ptnr3_label_atom_id>
<PDBx:ptnr3_label_comp_id>HOH</PDBx:ptnr3_label_comp_id>
<PDBx:ptnr3_label_seq_id>3001</PDBx:ptnr3_label_seq_id>
<PDBx:value>95.5</PDBx:value>
</PDBx:pdbx_struct_conn_angle>
<PDBx:pdbx_struct_conn_angle id="13">
<PDBx:ptnr1_PDB_ins_code></PDBx:ptnr1_PDB_ins_code>
<PDBx:ptnr1_label_asym_id>A</PDBx:ptnr1_label_asym_id>
<PDBx:ptnr1_label_atom_id>OE</PDBx:ptnr1_label_atom_id>
<PDBx:ptnr1_label_comp_id>GLU</PDBx:ptnr1_label_comp_id>
<PDBx:ptnr1_label_seq_id>160</PDBx:ptnr1_label_seq_id>
<PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code>
<PDBx:ptnr2_label_asym_id>A</PDBx:ptnr2_label_asym_id>
<PDBx:ptnr2_label_atom_id></PDBx:ptnr2_label_atom_id>
<PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id>
<PDBx:ptnr2_label_seq_id>501</PDBx:ptnr2_label_seq_id>
<PDBx:ptnr3_PDB_ins_code>O</PDBx:ptnr3_PDB_ins_code>
<PDBx:ptnr3_label_asym_id>A</PDBx:ptnr3_label_asym_id>
<PDBx:ptnr3_label_atom_id></PDBx:ptnr3_label_atom_id>
<PDBx:ptnr3_label_comp_id>HOH</PDBx:ptnr3_label_comp_id>
<PDBx:ptnr3_label_seq_id>3001</PDBx:ptnr3_label_seq_id>
<PDBx:value>109.4</PDBx:value>
</PDBx:pdbx_struct_conn_angle>
<PDBx:pdbx_struct_conn_angle id="14">
<PDBx:ptnr1_PDB_ins_code></PDBx:ptnr1_PDB_ins_code>
<PDBx:ptnr1_label_asym_id>A</PDBx:ptnr1_label_asym_id>
<PDBx:ptnr1_label_atom_id>OD</PDBx:ptnr1_label_atom_id>
<PDBx:ptnr1_label_comp_id>ASP</PDBx:ptnr1_label_comp_id>
<PDBx:ptnr1_label_seq_id>125</PDBx:ptnr1_label_seq_id>
<PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code>
<PDBx:ptnr2_label_asym_id>A</PDBx:ptnr2_label_asym_id>
<PDBx:ptnr2_label_atom_id></PDBx:ptnr2_label_atom_id>
<PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id>
<PDBx:ptnr2_label_seq_id>501</PDBx:ptnr2_label_seq_id>
<PDBx:ptnr3_PDB_ins_code>NE</PDBx:ptnr3_PDB_ins_code>
<PDBx:ptnr3_label_asym_id>A</PDBx:ptnr3_label_asym_id>
<PDBx:ptnr3_label_atom_id></PDBx:ptnr3_label_atom_id>
<PDBx:ptnr3_label_comp_id>HIS</PDBx:ptnr3_label_comp_id>
<PDBx:ptnr3_label_seq_id>421</PDBx:ptnr3_label_seq_id>
<PDBx:value>90.4</PDBx:value>
</PDBx:pdbx_struct_conn_angle>
<PDBx:pdbx_struct_conn_angle id="15">
<PDBx:ptnr1_PDB_ins_code></PDBx:ptnr1_PDB_ins_code>
<PDBx:ptnr1_label_asym_id>A</PDBx:ptnr1_label_asym_id>
<PDBx:ptnr1_label_atom_id>OE</PDBx:ptnr1_label_atom_id>
<PDBx:ptnr1_label_comp_id>GLU</PDBx:ptnr1_label_comp_id>
<PDBx:ptnr1_label_seq_id>160</PDBx:ptnr1_label_seq_id>
<PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code>
<PDBx:ptnr2_label_asym_id>A</PDBx:ptnr2_label_asym_id>
<PDBx:ptnr2_label_atom_id></PDBx:ptnr2_label_atom_id>
<PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id>
<PDBx:ptnr2_label_seq_id>501</PDBx:ptnr2_label_seq_id>
<PDBx:ptnr3_PDB_ins_code>NE</PDBx:ptnr3_PDB_ins_code>
<PDBx:ptnr3_label_asym_id>A</PDBx:ptnr3_label_asym_id>
<PDBx:ptnr3_label_atom_id></PDBx:ptnr3_label_atom_id>
<PDBx:ptnr3_label_comp_id>HIS</PDBx:ptnr3_label_comp_id>
<PDBx:ptnr3_label_seq_id>421</PDBx:ptnr3_label_seq_id>
<PDBx:value>111.3</PDBx:value>
</PDBx:pdbx_struct_conn_angle>
<PDBx:pdbx_struct_conn_angle id="16">
<PDBx:ptnr1_PDB_ins_code></PDBx:ptnr1_PDB_ins_code>
<PDBx:ptnr1_label_asym_id>A</PDBx:ptnr1_label_asym_id>
<PDBx:ptnr1_label_atom_id>O</PDBx:ptnr1_label_atom_id>
<PDBx:ptnr1_label_comp_id>HOH</PDBx:ptnr1_label_comp_id>
<PDBx:ptnr1_label_seq_id>3001</PDBx:ptnr1_label_seq_id>
<PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code>
<PDBx:ptnr2_label_asym_id>A</PDBx:ptnr2_label_asym_id>
<PDBx:ptnr2_label_atom_id></PDBx:ptnr2_label_atom_id>
<PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id>
<PDBx:ptnr2_label_seq_id>501</PDBx:ptnr2_label_seq_id>
<PDBx:ptnr3_PDB_ins_code>NE</PDBx:ptnr3_PDB_ins_code>
<PDBx:ptnr3_label_asym_id>A</PDBx:ptnr3_label_asym_id>
<PDBx:ptnr3_label_atom_id></PDBx:ptnr3_label_atom_id>
<PDBx:ptnr3_label_comp_id>HIS</PDBx:ptnr3_label_comp_id>
<PDBx:ptnr3_label_seq_id>421</PDBx:ptnr3_label_seq_id>
<PDBx:value>138.9</PDBx:value>
</PDBx:pdbx_struct_conn_angle>
<PDBx:pdbx_struct_conn_angle id="17">
<PDBx:ptnr1_PDB_ins_code></PDBx:ptnr1_PDB_ins_code>
<PDBx:ptnr1_label_asym_id>B</PDBx:ptnr1_label_asym_id>
<PDBx:ptnr1_label_atom_id>O</PDBx:ptnr1_label_atom_id>
<PDBx:ptnr1_label_comp_id>HOH</PDBx:ptnr1_label_comp_id>
<PDBx:ptnr1_label_seq_id>3001</PDBx:ptnr1_label_seq_id>
<PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code>
<PDBx:ptnr2_label_asym_id>B</PDBx:ptnr2_label_asym_id>
<PDBx:ptnr2_label_atom_id></PDBx:ptnr2_label_atom_id>
<PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id>
<PDBx:ptnr2_label_seq_id>500</PDBx:ptnr2_label_seq_id>
<PDBx:ptnr3_PDB_ins_code>NE</PDBx:ptnr3_PDB_ins_code>
<PDBx:ptnr3_label_asym_id>B</PDBx:ptnr3_label_asym_id>
<PDBx:ptnr3_label_atom_id></PDBx:ptnr3_label_atom_id>
<PDBx:ptnr3_label_comp_id>HIS</PDBx:ptnr3_label_comp_id>
<PDBx:ptnr3_label_seq_id>114</PDBx:ptnr3_label_seq_id>
<PDBx:value>106.4</PDBx:value>
</PDBx:pdbx_struct_conn_angle>
<PDBx:pdbx_struct_conn_angle id="18">
<PDBx:ptnr1_PDB_ins_code></PDBx:ptnr1_PDB_ins_code>
<PDBx:ptnr1_label_asym_id>B</PDBx:ptnr1_label_asym_id>
<PDBx:ptnr1_label_atom_id>O</PDBx:ptnr1_label_atom_id>
<PDBx:ptnr1_label_comp_id>HOH</PDBx:ptnr1_label_comp_id>
<PDBx:ptnr1_label_seq_id>3001</PDBx:ptnr1_label_seq_id>
<PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code>
<PDBx:ptnr2_label_asym_id>B</PDBx:ptnr2_label_asym_id>
<PDBx:ptnr2_label_atom_id></PDBx:ptnr2_label_atom_id>
<PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id>
<PDBx:ptnr2_label_seq_id>500</PDBx:ptnr2_label_seq_id>
<PDBx:ptnr3_PDB_ins_code>OD</PDBx:ptnr3_PDB_ins_code>
<PDBx:ptnr3_label_asym_id>B</PDBx:ptnr3_label_asym_id>
<PDBx:ptnr3_label_atom_id></PDBx:ptnr3_label_atom_id>
<PDBx:ptnr3_label_comp_id>ASP</PDBx:ptnr3_label_comp_id>
<PDBx:ptnr3_label_seq_id>125</PDBx:ptnr3_label_seq_id>
<PDBx:value>100.5</PDBx:value>
</PDBx:pdbx_struct_conn_angle>
<PDBx:pdbx_struct_conn_angle id="19">
<PDBx:ptnr1_PDB_ins_code></PDBx:ptnr1_PDB_ins_code>
<PDBx:ptnr1_label_asym_id>B</PDBx:ptnr1_label_asym_id>
<PDBx:ptnr1_label_atom_id>NE</PDBx:ptnr1_label_atom_id>
<PDBx:ptnr1_label_comp_id>HIS</PDBx:ptnr1_label_comp_id>
<PDBx:ptnr1_label_seq_id>114</PDBx:ptnr1_label_seq_id>
<PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code>
<PDBx:ptnr2_label_asym_id>B</PDBx:ptnr2_label_asym_id>
<PDBx:ptnr2_label_atom_id></PDBx:ptnr2_label_atom_id>
<PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id>
<PDBx:ptnr2_label_seq_id>500</PDBx:ptnr2_label_seq_id>
<PDBx:ptnr3_PDB_ins_code>OD</PDBx:ptnr3_PDB_ins_code>
<PDBx:ptnr3_label_asym_id>B</PDBx:ptnr3_label_asym_id>
<PDBx:ptnr3_label_atom_id></PDBx:ptnr3_label_atom_id>
<PDBx:ptnr3_label_comp_id>ASP</PDBx:ptnr3_label_comp_id>
<PDBx:ptnr3_label_seq_id>125</PDBx:ptnr3_label_seq_id>
<PDBx:value>115.6</PDBx:value>
</PDBx:pdbx_struct_conn_angle>
<PDBx:pdbx_struct_conn_angle id="20">
<PDBx:ptnr1_PDB_ins_code></PDBx:ptnr1_PDB_ins_code>
<PDBx:ptnr1_label_asym_id>B</PDBx:ptnr1_label_asym_id>
<PDBx:ptnr1_label_atom_id>O</PDBx:ptnr1_label_atom_id>
<PDBx:ptnr1_label_comp_id>HOH</PDBx:ptnr1_label_comp_id>
<PDBx:ptnr1_label_seq_id>3001</PDBx:ptnr1_label_seq_id>
<PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code>
<PDBx:ptnr2_label_asym_id>B</PDBx:ptnr2_label_asym_id>
<PDBx:ptnr2_label_atom_id></PDBx:ptnr2_label_atom_id>
<PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id>
<PDBx:ptnr2_label_seq_id>500</PDBx:ptnr2_label_seq_id>
<PDBx:ptnr3_PDB_ins_code>NE</PDBx:ptnr3_PDB_ins_code>
<PDBx:ptnr3_label_asym_id>B</PDBx:ptnr3_label_asym_id>
<PDBx:ptnr3_label_atom_id></PDBx:ptnr3_label_atom_id>
<PDBx:ptnr3_label_comp_id>HIS</PDBx:ptnr3_label_comp_id>
<PDBx:ptnr3_label_seq_id>226</PDBx:ptnr3_label_seq_id>
<PDBx:value>123.2</PDBx:value>
</PDBx:pdbx_struct_conn_angle>
<PDBx:pdbx_struct_conn_angle id="21">
<PDBx:ptnr1_PDB_ins_code></PDBx:ptnr1_PDB_ins_code>
<PDBx:ptnr1_label_asym_id>B</PDBx:ptnr1_label_asym_id>
<PDBx:ptnr1_label_atom_id>NE</PDBx:ptnr1_label_atom_id>
<PDBx:ptnr1_label_comp_id>HIS</PDBx:ptnr1_label_comp_id>
<PDBx:ptnr1_label_seq_id>114</PDBx:ptnr1_label_seq_id>
<PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code>
<PDBx:ptnr2_label_asym_id>B</PDBx:ptnr2_label_asym_id>
<PDBx:ptnr2_label_atom_id></PDBx:ptnr2_label_atom_id>
<PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id>
<PDBx:ptnr2_label_seq_id>500</PDBx:ptnr2_label_seq_id>
<PDBx:ptnr3_PDB_ins_code>NE</PDBx:ptnr3_PDB_ins_code>
<PDBx:ptnr3_label_asym_id>B</PDBx:ptnr3_label_asym_id>
<PDBx:ptnr3_label_atom_id></PDBx:ptnr3_label_atom_id>
<PDBx:ptnr3_label_comp_id>HIS</PDBx:ptnr3_label_comp_id>
<PDBx:ptnr3_label_seq_id>226</PDBx:ptnr3_label_seq_id>
<PDBx:value>123.2</PDBx:value>
</PDBx:pdbx_struct_conn_angle>
<PDBx:pdbx_struct_conn_angle id="22">
<PDBx:ptnr1_PDB_ins_code></PDBx:ptnr1_PDB_ins_code>
<PDBx:ptnr1_label_asym_id>B</PDBx:ptnr1_label_asym_id>
<PDBx:ptnr1_label_atom_id>OD</PDBx:ptnr1_label_atom_id>
<PDBx:ptnr1_label_comp_id>ASP</PDBx:ptnr1_label_comp_id>
<PDBx:ptnr1_label_seq_id>125</PDBx:ptnr1_label_seq_id>
<PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code>
<PDBx:ptnr2_label_asym_id>B</PDBx:ptnr2_label_asym_id>
<PDBx:ptnr2_label_atom_id></PDBx:ptnr2_label_atom_id>
<PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id>
<PDBx:ptnr2_label_seq_id>500</PDBx:ptnr2_label_seq_id>
<PDBx:ptnr3_PDB_ins_code>NE</PDBx:ptnr3_PDB_ins_code>
<PDBx:ptnr3_label_asym_id>B</PDBx:ptnr3_label_asym_id>
<PDBx:ptnr3_label_atom_id></PDBx:ptnr3_label_atom_id>
<PDBx:ptnr3_label_comp_id>HIS</PDBx:ptnr3_label_comp_id>
<PDBx:ptnr3_label_seq_id>226</PDBx:ptnr3_label_seq_id>
<PDBx:value>82.7</PDBx:value>
</PDBx:pdbx_struct_conn_angle>
<PDBx:pdbx_struct_conn_angle id="23">
<PDBx:ptnr1_PDB_ins_code></PDBx:ptnr1_PDB_ins_code>
<PDBx:ptnr1_label_asym_id>B</PDBx:ptnr1_label_asym_id>
<PDBx:ptnr1_label_atom_id>OE</PDBx:ptnr1_label_atom_id>
<PDBx:ptnr1_label_comp_id>GLU</PDBx:ptnr1_label_comp_id>
<PDBx:ptnr1_label_seq_id>160</PDBx:ptnr1_label_seq_id>
<PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code>
<PDBx:ptnr2_label_asym_id>B</PDBx:ptnr2_label_asym_id>
<PDBx:ptnr2_label_atom_id></PDBx:ptnr2_label_atom_id>
<PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id>
<PDBx:ptnr2_label_seq_id>501</PDBx:ptnr2_label_seq_id>
<PDBx:ptnr3_PDB_ins_code>OD</PDBx:ptnr3_PDB_ins_code>
<PDBx:ptnr3_label_asym_id>B</PDBx:ptnr3_label_asym_id>
<PDBx:ptnr3_label_atom_id></PDBx:ptnr3_label_atom_id>
<PDBx:ptnr3_label_comp_id>ASP</PDBx:ptnr3_label_comp_id>
<PDBx:ptnr3_label_seq_id>125</PDBx:ptnr3_label_seq_id>
<PDBx:value>148.6</PDBx:value>
</PDBx:pdbx_struct_conn_angle>
</PDBx:pdbx_struct_conn_angleCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
1
1
1
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
1
1
1
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
pdbx_struct_conn_angleCategory
This property indicates that datablock
has a category element pdbx_struct_conn_angle.
pdbx_struct_conn_angleItem
Abstract Datatype property for pdbx_struct_conn_angle items.
reference_to_pdbx_struct_conn_angle
cross-reference to pdbx_struct_conn_angle
pdbx_struct_conn_angle.ptnr1_PDB_ins_code
A component of the identifier for partner 1 of the structure angle.
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the
ATOM_SITE category.
pdbx_struct_conn_angle.ptnr1_auth_alt_id
A component of the identifier for partner 1 of the structure angle.
This data item is a pointer to attribute pdbx_auth_alt_id in category atom_site
in the ATOM_SITE category.
pdbx_struct_conn_angle.ptnr1_auth_asym_id
A component of the identifier for partner 1 of the structure angle.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_conn_angle.ptnr1_auth_atom_id
A component of the identifier for partner 1 of the structure angle.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_conn_angle.ptnr1_auth_comp_id
A component of the identifier for partner 1 of the structure angle.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_conn_angle.ptnr1_auth_seq_id
A component of the identifier for partner 1 of the structure angle.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_conn_angle.ptnr1_label_alt_id
A component of the identifier for partner 1 of the structure
angle.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_conn_angle.ptnr1_label_asym_id
A component of the identifier for partner 1 of the structure angle.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_conn_angle.ptnr1_label_atom_id
A component of the identifier for partner 1 of the structure angle.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_conn_angle.ptnr1_label_comp_id
A component of the identifier for partner 1 of the structure angle.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_conn_angle.ptnr1_label_seq_id
A component of the identifier for partner 1 of the structure angle.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_conn_angle.ptnr1_symmetry
Describes the symmetry operation that should be applied to the
atom specified by attribute ptnr1_label* in category pdbx_struct_conn_angle to generate the
first partner in the structure angle.
7th symm. posn.; +a on x; -b on y
7_645
pdbx_struct_conn_angle.ptnr2_PDB_ins_code
A component of the identifier for partner 1 of the structure angle.
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the
ATOM_SITE category.
pdbx_struct_conn_angle.ptnr2_auth_alt_id
A component of the identifier for partner 2 of the structure angle.
This data item is a pointer to attribute pdbx_auth_alt_id in category atom_site in
the ATOM_SITE category.
pdbx_struct_conn_angle.ptnr2_auth_asym_id
A component of the identifier for partner 2 of the structure angle.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_conn_angle.ptnr2_auth_atom_id
A component of the identifier for partner 2 of the structure angle.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_conn_angle.ptnr2_auth_comp_id
A component of the identifier for partner 2 of the structure angle.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_conn_angle.ptnr2_auth_seq_id
A component of the identifier for partner 2 of the structure angle.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_conn_angle.ptnr2_label_alt_id
A component of the identifier for partner 2 of the structure angle.
This data item is a pointer to attribute label_alt.id in category atom_site in the
ATOM_SITE category.
pdbx_struct_conn_angle.ptnr2_label_asym_id
A component of the identifier for partner 2 of the structure angle.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_conn_angle.ptnr2_label_atom_id
A component of the identifier for partner 2 of the structure angle.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_conn_angle.ptnr2_label_comp_id
A component of the identifier for partner 2 of the structure angle.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_conn_angle.ptnr2_label_seq_id
A component of the identifier for partner 2 of the structure angle.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_conn_angle.ptnr2_symmetry
Describes the symmetry operation that should be applied to the
atom specified by attribute ptnr2_label* in category pdbx_struct_conn_angle to generate the
second partner in the structure angle.
pdbx_struct_conn_angle.ptnr3_PDB_ins_code
A component of the identifier for partner 3 of the structure angle.
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in
the ATOM_SITE category.
pdbx_struct_conn_angle.ptnr3_auth_alt_id
A component of the identifier for partner 3 of the structure angle.
This data item is a pointer to attribute pdbx_auth_alt_id in category atom_site in
the ATOM_SITE category.
pdbx_struct_conn_angle.ptnr3_auth_asym_id
A component of the identifier for partner 3 of the structure angle.
This data item is a pointer to attribute auth_asym_id in category atom_site in
the ATOM_SITE category.
pdbx_struct_conn_angle.ptnr3_auth_atom_id
A component of the identifier for partner 3 of the
structure angle.
This data item is a pointer to attribute auth_atom_id in category atom_site in
the ATOM_SITE category.
pdbx_struct_conn_angle.ptnr3_auth_comp_id
A component of the identifier for partner 3 of the structure angle.
This data item is a pointer to attribute auth_comp_id in category atom_site in
the ATOM_SITE category.
pdbx_struct_conn_angle.ptnr3_auth_seq_id
A component of the identifier for partner 1 of the structure angle.
This data item is a pointer to attribute auth_seq_id in category atom_site in
the ATOM_SITE category.
pdbx_struct_conn_angle.ptnr3_label_alt_id
A component of the identifier for partner 3 of the structure angle.
This data item is a pointer to attribute label_alt_id in category atom_site in
the ATOM_SITE category.
pdbx_struct_conn_angle.ptnr3_label_asym_id
A component of the identifier for partner 3 of the structure angle.
This data item is a pointer to attribute label_asym_id in category atom_site in
the ATOM_SITE category.
pdbx_struct_conn_angle.ptnr3_label_atom_id
A component of the identifier for partner 3 of the structure angle.
This data item is a pointer to attribute label_atom_id in category atom_site in
the ATOM_SITE category.
pdbx_struct_conn_angle.ptnr3_label_comp_id
A component of the identifier for partner 3 of the structure angle.
This data item is a pointer to attribute label_comp_id in category atom_site in
the ATOM_SITE category.
pdbx_struct_conn_angle.ptnr3_label_seq_id
A component of the identifier for partner 1 of the structure angle.
This data item is a pointer to attribute label_seq_id in category atom_site in
the ATOM_SITE category.
pdbx_struct_conn_angle.value
Angle in degrees defined by the three sites
attribute ptnr1_label_atom_id,
in category pdbx_struct_conn_angle attribute ptnr2_label_atom_id
in category pdbx_struct_conn_angle attribute ptnr3_label_atom_id
in category pdbx_struct_conn_angle
pdbx_struct_conn_angle.value_esd
The standard uncertainty (estimated standard deviation)
of attribute value in category pdbx_struct_conn_angle
pdbx_struct_conn_angle.id
The value of attribute id in category pdbx_struct_conn_angle must uniquely identify a record in
the PDBX_STRUCT_CONN_ANGLE list.
Note that this item need not be a number; it can be any unique
identifier.
pdbx_struct_entity_inst
Data items in the PDBX_STRUCT_ENTITY_INST category record details about the
structural elements in the deposited entry. The entity instance is a method
neutral identifier for the observed molecular entities in the deposited coordinate
set.
Example 1 -
<PDBx:pdbx_struct_entity_instCategory>
<PDBx:pdbx_struct_entity_inst id="A">
<PDBx:details>one monomer of the dimeric enzyme</PDBx:details>
<PDBx:entity_id>1</PDBx:entity_id>
</PDBx:pdbx_struct_entity_inst>
<PDBx:pdbx_struct_entity_inst id="B">
<PDBx:details>one monomer of the dimeric enzyme</PDBx:details>
<PDBx:entity_id>1</PDBx:entity_id>
</PDBx:pdbx_struct_entity_inst>
</PDBx:pdbx_struct_entity_instCategory>
0
1
0
1
1
pdbx_struct_entity_instCategory
This property indicates that datablock
has a category element pdbx_struct_entity_inst.
pdbx_struct_entity_instItem
Abstract Datatype property for pdbx_struct_entity_inst items.
reference_to_pdbx_struct_entity_inst
cross-reference to pdbx_struct_entity_inst
pdbx_struct_entity_inst.details
A description of special aspects of this portion of the contents
of the deposited unit.
The drug binds to this enzyme in two roughly
twofold symmetric modes. Hence this
biological unit (3) is roughly twofold
symmetric to biological unit (2). Disorder in
the protein chain indicated with alternative
ID 2 should be used with this biological unit.
pdbx_struct_entity_inst.entity_id
This data item is a pointer to attribute id in category entity in the ENTITY category.
pdbx_struct_entity_inst.id
The value of attribute id in category pdbx_struct_entity_inst must uniquely identify a record in
the PDBX_STRUCT_ENTITY_INST list.
The entity instance is a method neutral identifier for the observed
molecular entities in the deposited coordinate set.
1
A
2B3
pdbx_struct_info
Special features of this structural entry.
Example 1 -
<PDBx:pdbx_struct_infoCategory>
<PDBx:pdbx_struct_info type="nonpolymer_zero_occupancy_flag" value="Y"></PDBx:pdbx_struct_info>
<PDBx:pdbx_struct_info type="polymer_zero_occupancy_flag" value="Y"></PDBx:pdbx_struct_info>
<PDBx:pdbx_struct_info type="multiple_model_flag" value="Y"></PDBx:pdbx_struct_info>
<PDBx:pdbx_struct_info type="multiple_model_details" value="Model 3 missing ligand ACX"></PDBx:pdbx_struct_info>
<PDBx:pdbx_struct_info type="nonpolymer_details" value="Disordered ligand geometry for C34 with missing pyridine ring"></PDBx:pdbx_struct_info>
<PDBx:pdbx_struct_info type="missing atoms in alternate conformations" value="Y"></PDBx:pdbx_struct_info>
</PDBx:pdbx_struct_infoCategory>
0
1
1
1
pdbx_struct_infoCategory
This property indicates that datablock
has a category element pdbx_struct_info.
pdbx_struct_infoItem
Abstract Datatype property for pdbx_struct_info items.
reference_to_pdbx_struct_info
cross-reference to pdbx_struct_info
pdbx_struct_info.details
Additional details about this information item.
nonpolymer_zero_occupancy_flag
polymer_zero_occupancy_flag
multiple_model_flag
multiple_model_details
nonpolymer_details
missing atoms in alternate conformations
The information category/type for this item.
pdbx_struct_info.value
The value of this information item.
pdbx_struct_legacy_oper_list
Data items in the PDBX_STRUCT_LEGACY_OPER_LIST category describe
Cartesian rotation and translation operations required to
generate or transform the coordinates deposited with this entry.
This category provides a container for matrices used to construct
icosahedral assemblies in legacy entries.
Example 1 -
<PDBx:pdbx_struct_legacy_oper_listCategory>
<PDBx:pdbx_struct_legacy_oper_list id="2">
<PDBx:matrix11>0.247</PDBx:matrix11>
<PDBx:matrix12>0.935</PDBx:matrix12>
<PDBx:matrix13>0.256</PDBx:matrix13>
<PDBx:matrix21>0.929</PDBx:matrix21>
<PDBx:matrix22>0.153</PDBx:matrix22>
<PDBx:matrix23>0.337</PDBx:matrix23>
<PDBx:matrix31>0.276</PDBx:matrix31>
<PDBx:matrix32>0.321</PDBx:matrix32>
<PDBx:matrix33>-0.906</PDBx:matrix33>
<PDBx:vector1>-8.253</PDBx:vector1>
<PDBx:vector2>-11.743</PDBx:vector2>
<PDBx:vector3>-1.782</PDBx:vector3>
</PDBx:pdbx_struct_legacy_oper_list>
</PDBx:pdbx_struct_legacy_oper_listCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
pdbx_struct_legacy_oper_listCategory
This property indicates that datablock
has a category element pdbx_struct_legacy_oper_list.
pdbx_struct_legacy_oper_listItem
Abstract Datatype property for pdbx_struct_legacy_oper_list items.
reference_to_pdbx_struct_legacy_oper_list
cross-reference to pdbx_struct_legacy_oper_list
pdbx_struct_legacy_oper_list.matrix11
The [1][1] element of the 3x3 matrix component of the
transformation operation.
pdbx_struct_legacy_oper_list.matrix12
The [1][2] element of the 3x3 matrix component of the
transformation operation.
pdbx_struct_legacy_oper_list.matrix13
The [1][3] element of the 3x3 matrix component of the
transformation operation.
pdbx_struct_legacy_oper_list.matrix21
The [2][1] element of the 3x3 matrix component of the
transformation operation.
pdbx_struct_legacy_oper_list.matrix22
The [2][2] element of the 3x3 matrix component of the
transformation operation.
pdbx_struct_legacy_oper_list.matrix23
The [2][3] element of the 3x3 matrix component of the
transformation operation.
pdbx_struct_legacy_oper_list.matrix31
The [3][1] element of the 3x3 matrix component of the
transformation operation.
pdbx_struct_legacy_oper_list.matrix32
The [3][2] element of the 3x3 matrix component of the
transformation operation.
pdbx_struct_legacy_oper_list.matrix33
The [3][3] element of the 3x3 matrix component of the
transformation operation.
pdbx_struct_legacy_oper_list.name
A descriptive name for the transformation operation.
identity matrix
two-fold rotation
pdbx_struct_legacy_oper_list.vector1
The [1] element of the three-element vector component of the
transformation operation.
pdbx_struct_legacy_oper_list.vector2
The [2] element of the three-element vector component of the
transformation operation.
pdbx_struct_legacy_oper_list.vector3
The [3] element of the three-element vector component of the
transformation operation.
pdbx_struct_legacy_oper_list.id
This integer value must uniquely identify a
record in the PDBX_STRUCT_LEGACY_OPER_LIST list.
pdbx_struct_mod_residue
Data items in the PDBX_STRUCT_MOD_RESIDUE category list the
modified polymer components in the entry and provide some
details describing the nature of the modification.
Example 1
<PDBx:pdbx_struct_mod_residueCategory>
<PDBx:pdbx_struct_mod_residue id="1">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_comp_id>CRW</PDBx:auth_comp_id>
<PDBx:auth_seq_id>66</PDBx:auth_seq_id>
<PDBx:details>CIRCULARIZED TRI-PEPTIDE CHROMOPHORE</PDBx:details>
<PDBx:parent_comp_id>ALA</PDBx:parent_comp_id>
</PDBx:pdbx_struct_mod_residue>
<PDBx:pdbx_struct_mod_residue id="2">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_comp_id>CRW</PDBx:auth_comp_id>
<PDBx:auth_seq_id>66</PDBx:auth_seq_id>
<PDBx:details>CIRCULARIZED TRI-PEPTIDE CHROMOPHORE</PDBx:details>
<PDBx:parent_comp_id>SER</PDBx:parent_comp_id>
</PDBx:pdbx_struct_mod_residue>
<PDBx:pdbx_struct_mod_residue id="3">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_comp_id>CRW</PDBx:auth_comp_id>
<PDBx:auth_seq_id>66</PDBx:auth_seq_id>
<PDBx:details>CIRCULARIZED TRI-PEPTIDE CHROMOPHORE</PDBx:details>
<PDBx:parent_comp_id>GLY</PDBx:parent_comp_id>
</PDBx:pdbx_struct_mod_residue>
</PDBx:pdbx_struct_mod_residueCategory>
0
1
0
1
1
1
1
1
1
1
0
1
0
1
0
1
0
1
0
1
1
pdbx_struct_mod_residueCategory
This property indicates that datablock
has a category element pdbx_struct_mod_residue.
pdbx_struct_mod_residueItem
Abstract Datatype property for pdbx_struct_mod_residue items.
reference_to_pdbx_struct_mod_residue
cross-reference to pdbx_struct_mod_residue
pdbx_struct_mod_residue.PDB_ins_code
Part of the identifier for the modified polymer component.
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the
ATOM_SITE category.
pdbx_struct_mod_residue.PDB_model_num
Part of the identifier for the modified polymer component.
This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the
ATOM_SITE category.
pdbx_struct_mod_residue.auth_asym_id
Part of the identifier for the modified polymer component.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_mod_residue.auth_comp_id
Part of the identifier for the modified polymer component.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_mod_residue.auth_seq_id
Part of the identifier for the modified polymer component.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_mod_residue.details
Details of the modification for this polymer component.
pdbx_struct_mod_residue.label_asym_id
Part of the identifier for the modified polymer component.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_mod_residue.label_comp_id
Part of the identifier for the modified polymer component.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_mod_residue.label_seq_id
Part of the identifier for the unobserved or zero occupancy residue.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_mod_residue.parent_comp_id
The parent component identifier for this modified polymer component.
pdbx_struct_mod_residue.id
The value of attribute id in category pdbx_struct_mod_residue must uniquely identify
each item in the PDBX_STRUCT_MOD_RESIDUE list.
This is an integer serial number.
pdbx_struct_msym_gen
Data items in the PDBX_STRUCT_MSYM_GEN category record details about
the generation of the minimal asymmetric unit. For instance, this
category can be used to provide this information for helical and point
symmetry systems. The PDBX_STRUCT_MSYM_GEN data items provide the
specifications of the components that constitute the asymmetric unit
in terms of cartesian transformations of deposited coordinates.
Example 1 -
<PDBx:pdbx_struct_msym_genCategory>
<PDBx:pdbx_struct_msym_gen entity_inst_id="A" msym_id="A" oper_expression="3"></PDBx:pdbx_struct_msym_gen>
<PDBx:pdbx_struct_msym_gen entity_inst_id="B" msym_id="B" oper_expression="4"></PDBx:pdbx_struct_msym_gen>
<PDBx:pdbx_struct_msym_gen entity_inst_id="B" msym_id="C" oper_expression="5"></PDBx:pdbx_struct_msym_gen>
</PDBx:pdbx_struct_msym_genCategory>
1
1
1
pdbx_struct_msym_genCategory
This property indicates that datablock
has a category element pdbx_struct_msym_gen.
pdbx_struct_msym_genItem
Abstract Datatype property for pdbx_struct_msym_gen items.
reference_to_pdbx_struct_msym_gen
cross-reference to pdbx_struct_msym_gen
pdbx_struct_msym_gen.entity_inst_id
This data item is a pointer to attribute id in category pdbx_struct_entity_inst in
the PDBX_STRUCT_ENTITY_INST category.
pdbx_struct_msym_gen.msym_id
Uniquely identifies the this structure instance in
point symmetry unit.
pdbx_struct_msym_gen.oper_expression
Identifies the operation from category PDBX_STRUCT_OPER_LIST.
(1)
(1-3)
pdbx_struct_oper_list
Data items in the PDBX_STRUCT_OPER_LIST category describe
Cartesian rotation and translation operations required to
generate or transform the coordinates deposited with this entry.
Example 1 -
<PDBx:pdbx_struct_oper_listCategory>
<PDBx:pdbx_struct_oper_list id="2">
<PDBx:matrix11>0.247</PDBx:matrix11>
<PDBx:matrix12>0.935</PDBx:matrix12>
<PDBx:matrix13>0.256</PDBx:matrix13>
<PDBx:matrix21>0.929</PDBx:matrix21>
<PDBx:matrix22>0.153</PDBx:matrix22>
<PDBx:matrix23>0.337</PDBx:matrix23>
<PDBx:matrix31>0.276</PDBx:matrix31>
<PDBx:matrix32>0.321</PDBx:matrix32>
<PDBx:matrix33>-0.906</PDBx:matrix33>
<PDBx:type>point symmetry operation</PDBx:type>
<PDBx:vector1>-8.253</PDBx:vector1>
<PDBx:vector2>-11.743</PDBx:vector2>
<PDBx:vector3>-1.782</PDBx:vector3>
</PDBx:pdbx_struct_oper_list>
</PDBx:pdbx_struct_oper_listCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
0
1
0
1
0
1
1
pdbx_struct_oper_listCategory
This property indicates that datablock
has a category element pdbx_struct_oper_list.
pdbx_struct_oper_listItem
Abstract Datatype property for pdbx_struct_oper_list items.
reference_to_pdbx_struct_oper_list
cross-reference to pdbx_struct_oper_list
pdbx_struct_oper_list.matrix11
The [1][1] element of the 3x3 matrix component of the
transformation operation.
pdbx_struct_oper_list.matrix12
The [1][2] element of the 3x3 matrix component of the
transformation operation.
pdbx_struct_oper_list.matrix13
The [1][3] element of the 3x3 matrix component of the
transformation operation.
pdbx_struct_oper_list.matrix21
The [2][1] element of the 3x3 matrix component of the
transformation operation.
pdbx_struct_oper_list.matrix22
The [2][2] element of the 3x3 matrix component of the
transformation operation.
pdbx_struct_oper_list.matrix23
The [2][3] element of the 3x3 matrix component of the
transformation operation.
pdbx_struct_oper_list.matrix31
The [3][1] element of the 3x3 matrix component of the
transformation operation.
pdbx_struct_oper_list.matrix32
The [3][2] element of the 3x3 matrix component of the
transformation operation.
pdbx_struct_oper_list.matrix33
The [3][3] element of the 3x3 matrix component of the
transformation operation.
pdbx_struct_oper_list.name
A descriptive name for the transformation operation.
1_555
two-fold rotation
pdbx_struct_oper_list.symmetry_operation
The symmetry operation corresponding to the transformation operation.
x,y,z
x+1/2,y,-z
identity operation
point symmetry operation
helical symmetry operation
crystal symmetry operation
3D crystal symmetry operation
2D crystal symmetry operation
transform to point frame
transform to helical frame
transform to crystal frame
transform to 2D crystal frame
transform to 3D crystal frame
build point asymmetric unit
build helical asymmetric unit
build 2D crystal asymmetric unit
build 3D crystal asymmetric unit
A code to indicate the type of operator.
pdbx_struct_oper_list.vector1
The [1] element of the three-element vector component of the
transformation operation.
pdbx_struct_oper_list.vector2
The [2] element of the three-element vector component of the
transformation operation.
pdbx_struct_oper_list.vector3
The [3] element of the three-element vector component of the
transformation operation.
pdbx_struct_oper_list.id
This identifier code must uniquely identify a
record in the PDBX_STRUCT_OPER_LIST list.
pdbx_struct_ref_seq_deletion
Data items in the PDBX_STRUCT_REF_SEQ_INSERTION category
annotate deletions in the sequence of the entity described
in the referenced database entry.
Example 1
<PDBx:pdbx_struct_ref_seq_deletionCategory>
<PDBx:pdbx_struct_ref_seq_deletion id="1">
<PDBx:asym_id>A</PDBx:asym_id>
<PDBx:comp_id>LEU</PDBx:comp_id>
<PDBx:db_code>P15456</PDBx:db_code>
<PDBx:db_name>UNP</PDBx:db_name>
<PDBx:db_seq_id>23</PDBx:db_seq_id>
<PDBx:details></PDBx:details>
</PDBx:pdbx_struct_ref_seq_deletion>
<PDBx:pdbx_struct_ref_seq_deletion id="1">
<PDBx:asym_id>A</PDBx:asym_id>
<PDBx:comp_id>THR</PDBx:comp_id>
<PDBx:db_code>P15456</PDBx:db_code>
<PDBx:db_name>UNP</PDBx:db_name>
<PDBx:db_seq_id>24</PDBx:db_seq_id>
<PDBx:details></PDBx:details>
</PDBx:pdbx_struct_ref_seq_deletion>
<PDBx:pdbx_struct_ref_seq_deletion id="1">
<PDBx:asym_id>A</PDBx:asym_id>
<PDBx:comp_id>GLN</PDBx:comp_id>
<PDBx:db_code>P15456</PDBx:db_code>
<PDBx:db_name>UNP</PDBx:db_name>
<PDBx:db_seq_id>25</PDBx:db_seq_id>
<PDBx:details></PDBx:details>
</PDBx:pdbx_struct_ref_seq_deletion>
</PDBx:pdbx_struct_ref_seq_deletionCategory>
1
1
1
1
1
1
1
1
1
1
0
1
1
pdbx_struct_ref_seq_deletionCategory
This property indicates that datablock
has a category element pdbx_struct_ref_seq_deletion.
pdbx_struct_ref_seq_deletionItem
Abstract Datatype property for pdbx_struct_ref_seq_deletion items.
reference_to_pdbx_struct_ref_seq_deletion
cross-reference to pdbx_struct_ref_seq_deletion
pdbx_struct_ref_seq_deletion.asym_id
Identifies the polymer entity instance in this entry corresponding
to the reference sequence in which the deletion is specified.
This data item is a pointer to attribute asym_id in category pdbx_poly_seq_scheme in the
PDBX_POLY_SEQ_SCHEME category.
pdbx_struct_ref_seq_deletion.comp_id
The monomer name found at this position in the referenced
database entry.
pdbx_struct_ref_seq_deletion.db_code
The code for this entity or biological unit or for a closely
related entity or biological unit in the named database.
pdbx_struct_ref_seq_deletion.db_name
The name of the database containing reference information about
this entity or biological unit.
pdbx_struct_ref_seq_deletion.db_seq_id
This data item is the database sequence numbering of the deleted
residue
pdbx_struct_ref_seq_deletion.details
A description of any special aspects of the deletion
pdbx_struct_ref_seq_deletion.id
The value of attribute id in category pdbx_struct_ref_seq_deletion must
uniquely identify a record in the PDBX_STRUCT_REF_SEQ_DELETION list.
pdbx_struct_ref_seq_feature
Data items in the PDBX_STRUCT_REF_SEQ_FEATURE category provide a
mechanism for identifying and annotating sequence features.
Example 1 -
<PDBx:pdbx_struct_ref_seq_featureCategory>
<PDBx:pdbx_struct_ref_seq_feature feature_id="1">
<PDBx:align_id>algn2</PDBx:align_id>
<PDBx:beg_auth_mon_id>GLU</PDBx:beg_auth_mon_id>
<PDBx:beg_auth_seq_id>10</PDBx:beg_auth_seq_id>
<PDBx:details> Special </PDBx:details>
<PDBx:end_auth_mon_id>PHE</PDBx:end_auth_mon_id>
<PDBx:end_auth_seq_id>14</PDBx:end_auth_seq_id>
<PDBx:type>variant</PDBx:type>
</PDBx:pdbx_struct_ref_seq_feature>
</PDBx:pdbx_struct_ref_seq_featureCategory>
1
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
pdbx_struct_ref_seq_featureCategory
This property indicates that datablock
has a category element pdbx_struct_ref_seq_feature.
pdbx_struct_ref_seq_featureItem
Abstract Datatype property for pdbx_struct_ref_seq_feature items.
reference_to_pdbx_struct_ref_seq_feature
cross-reference to pdbx_struct_ref_seq_feature
pdbx_struct_ref_seq_feature.align_id
This data item is a pointer to attribute align_id in category struct_ref_seq in
the STRUCT_REF_SEQ category.
pdbx_struct_ref_seq_feature.asym_id
Instance identifier for the polymer molecule.
A
B
pdbx_struct_ref_seq_feature.beg_auth_mon_id
Monomer ID at the initial position in the PDB sequence segment.
1
2
pdbx_struct_ref_seq_feature.beg_auth_seq_id
Initial position in the PDB sequence segment.
1
2
pdbx_struct_ref_seq_feature.beg_pdb_ins_code
Initial insertion code of the PDB sequence segment.
A
B
pdbx_struct_ref_seq_feature.beg_seq_num
Initial position in the sequence segment.
1
2
pdbx_struct_ref_seq_feature.details
A description of special aspects of the feature
pdbx_struct_ref_seq_feature.end_auth_mon_id
Monomer ID at the terminal position in the PDB sequence segment
1
2
pdbx_struct_ref_seq_feature.end_auth_seq_id
Ending position in the PDB sequence segment
1
2
pdbx_struct_ref_seq_feature.end_pdb_ins_code
Terminal insertion code of the PDB sequence segment.
A
B
pdbx_struct_ref_seq_feature.end_seq_num
Ending position in the sequence segment
1
2
pdbx_struct_ref_seq_feature.pdb_strand_id
PDB strand/chain id.
A
B
deletion
expression tag
variant
other
A classification of the feature
pdbx_struct_ref_seq_feature.feature_id
Uniquely identfies a sequence feature in
the STRUCT_REF_SEQ_FEATURE category.
pdbx_struct_ref_seq_feature_prop
Data items in the PDBX_STRUCT_REF_SEQ_FEATURE_PROP category provide a
mechanism for identifying and annotating properties of sequence features.
Example 1 -
<PDBx:pdbx_struct_ref_seq_feature_propCategory>
<PDBx:pdbx_struct_ref_seq_feature_prop feature_id="1" property_id="1">
<PDBx:beg_db_mon_id>GLU</PDBx:beg_db_mon_id>
<PDBx:beg_db_seq_id>100</PDBx:beg_db_seq_id>
<PDBx:details> Special splice at ... </PDBx:details>
<PDBx:end_db_mon_id>PHE</PDBx:end_db_mon_id>
<PDBx:end_db_seq_id>104</PDBx:end_db_seq_id>
<PDBx:type>VARIABLE_SPLICING</PDBx:type>
<PDBx:value>VSP_003456</PDBx:value>
</PDBx:pdbx_struct_ref_seq_feature_prop>
</PDBx:pdbx_struct_ref_seq_feature_propCategory>
0
1
0
1
0
1
0
1
0
1
1
1
1
1
1
1
pdbx_struct_ref_seq_feature_propCategory
This property indicates that datablock
has a category element pdbx_struct_ref_seq_feature_prop.
pdbx_struct_ref_seq_feature_propItem
Abstract Datatype property for pdbx_struct_ref_seq_feature_prop items.
reference_to_pdbx_struct_ref_seq_feature_prop
cross-reference to pdbx_struct_ref_seq_feature_prop
pdbx_struct_ref_seq_feature_prop.beg_db_mon_id
The begining monomer type found at the starting position
in the referenced database entry.
This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP
category.
pdbx_struct_ref_seq_feature_prop.beg_db_seq_id
The begining monomer sequence position
in the referenced database entry.
pdbx_struct_ref_seq_feature_prop.details
A description of special aspects of the property value pair.
pdbx_struct_ref_seq_feature_prop.end_db_mon_id
The terminal monomer type found at the ending position
in the referenced database entry.
This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP
category.
pdbx_struct_ref_seq_feature_prop.end_db_seq_id
The terminal monomer sequence position
in the referenced database entry.
pdbx_struct_ref_seq_feature_prop.type
Property type.
deletion', 'expression tag', 'variant', 'other
pdbx_struct_ref_seq_feature_prop.value
Property value.
pdbx_struct_ref_seq_feature_prop.feature_id
This data item is a pointer to attribute feature_id in category pdbx_struct_ref_seq_feature in
the STRUCT_REF_SEQ_FEATURE category.
pdbx_struct_ref_seq_feature_prop.property_id
This uniquely identifies the a property of a sequence feature in
the STRUCT_REF_SEQ_FEATURE_PROPx category.
pdbx_struct_ref_seq_insertion
Data items in the PDBX_STRUCT_REF_SEQ_INSERTION category
annotate insertions in the sequence of the entity described
in the referenced database entry.
Example 1
<PDBx:pdbx_struct_ref_seq_insertionCategory>
<PDBx:pdbx_struct_ref_seq_insertion id="1">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:asym_id>A</PDBx:asym_id>
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_seq_id>104</PDBx:auth_seq_id>
<PDBx:comp_id>GLY</PDBx:comp_id>
<PDBx:db_code>P00752</PDBx:db_code>
<PDBx:db_name>UNP</PDBx:db_name>
<PDBx:details>INSERTION</PDBx:details>
<PDBx:seq_id>102</PDBx:seq_id>
</PDBx:pdbx_struct_ref_seq_insertion>
<PDBx:pdbx_struct_ref_seq_insertion id="2">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:asym_id>A</PDBx:asym_id>
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_seq_id>105</PDBx:auth_seq_id>
<PDBx:comp_id>TRP</PDBx:comp_id>
<PDBx:db_code>P00752</PDBx:db_code>
<PDBx:db_name>UNP</PDBx:db_name>
<PDBx:details>INSERTION</PDBx:details>
<PDBx:seq_id>103</PDBx:seq_id>
</PDBx:pdbx_struct_ref_seq_insertion>
</PDBx:pdbx_struct_ref_seq_insertionCategory>
0
1
1
1
0
1
1
1
1
1
1
1
1
1
0
1
1
1
1
pdbx_struct_ref_seq_insertionCategory
This property indicates that datablock
has a category element pdbx_struct_ref_seq_insertion.
pdbx_struct_ref_seq_insertionItem
Abstract Datatype property for pdbx_struct_ref_seq_insertion items.
reference_to_pdbx_struct_ref_seq_insertion
cross-reference to pdbx_struct_ref_seq_insertion
pdbx_struct_ref_seq_insertion.PDB_ins_code
Part of the author identifier of the inserted residue.
This data item is a pointer to attribute pdb_ins_code in category pdbx_poly_seq_scheme in the
PDBX_POLY_SEQ_SCHEME category.
pdbx_struct_ref_seq_insertion.asym_id
Part of the identifier of the inserted residue.
This data item is a pointer to attribute asym_id in category pdbx_poly_seq_scheme in the
PDBX_POLY_SEQ_SCHEME category.
pdbx_struct_ref_seq_insertion.auth_asym_id
Part of the author identifier of the inserted residue.
This data item is a pointer to attribute pdb_strand_id in category pdbx_poly_seq_scheme in the
PDBX_POLY_SEQ_SCHEME category.
pdbx_struct_ref_seq_insertion.auth_seq_id
Part of the author identifier of the inserted residue.
This data item is a pointer to attribute auth_seq_num in category pdbx_poly_seq_scheme in the
PDBX_POLY_SEQ_SCHEME category.
pdbx_struct_ref_seq_insertion.comp_id
Part of the identifier of the inserted residue.
This data item is a pointer to attribute mon_id in category pdbx_poly_seq_scheme in the
PDBX_POLY_SEQ_SCHEME category.
pdbx_struct_ref_seq_insertion.db_code
The code for this entity or biological unit or for a closely
related entity or biological unit in the named database.
pdbx_struct_ref_seq_insertion.db_name
The name of the database containing reference information about
this entity or biological unit.
pdbx_struct_ref_seq_insertion.details
A description of any special aspects of the insertion
pdbx_struct_ref_seq_insertion.seq_id
Part of the author identifier of the inserted residue.
This data item is a pointer to attribute seq_id in category pdbx_poly_seq_scheme in the
PDBX_POLY_SEQ_SCHEME category.
pdbx_struct_ref_seq_insertion.id
The value of attribute id in category pdbx_struct_ref_seq_insertion must
uniquely identify a record in the PDBX_STRUCT_REF_SEQ_INSERTION list.
pdbx_struct_sheet_hbond
Data items in the PDBX_STRUCT_SHEET_HBOND category record details
about the hydrogen bonding between residue ranges in a beta sheet.
This category is provided for cases where only a single hydrogen
bond is used to register the two residue ranges. Category
STRUCT_SHEET_HBOND should be used when the initial and terminal
hydrogen bonds for strand pair are known.
0
1
0
1
0
1
0
1
0
1
0
1
1
1
0
1
1
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
0
1
1
1
1
1
1
pdbx_struct_sheet_hbondCategory
This property indicates that datablock
has a category element pdbx_struct_sheet_hbond.
pdbx_struct_sheet_hbondItem
Abstract Datatype property for pdbx_struct_sheet_hbond items.
reference_to_pdbx_struct_sheet_hbond
cross-reference to pdbx_struct_sheet_hbond
pdbx_struct_sheet_hbond.range_1_PDB_ins_code
A component of the residue identifier for the first partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_sheet_hbond.range_1_auth_asym_id
A component of the residue identifier for the first partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_sheet_hbond.range_1_auth_atom_id
A component of the residue identifier for the first partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_sheet_hbond.range_1_auth_comp_id
A component of the residue identifier for the first partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_sheet_hbond.range_1_auth_seq_id
A component of the residue identifier for the first partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_sheet_hbond.range_1_label_asym_id
A component of the residue identifier for the first partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_sheet_hbond.range_1_label_atom_id
A component of the residue identifier for the first partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_sheet_hbond.range_1_label_comp_id
A component of the residue identifier for the first partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_sheet_hbond.range_1_label_seq_id
A component of the residue identifier for the first partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_sheet_hbond.range_2_PDB_ins_code
A component of the residue identifier for the second partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_sheet_hbond.range_2_auth_asym_id
A component of the residue identifier for the second partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_sheet_hbond.range_2_auth_atom_id
A component of the residue identifier for the second partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_sheet_hbond.range_2_auth_comp_id
A component of the residue identifier for the second partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_sheet_hbond.range_2_auth_seq_id
A component of the residue identifier for the second partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_sheet_hbond.range_2_label_asym_id
A component of the residue identifier for the second partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_sheet_hbond.range_2_label_atom_id
A component of the residue identifier for the second partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_sheet_hbond.range_2_label_comp_id
A component of the residue identifier for the second partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_sheet_hbond.range_2_label_seq_id
A component of the residue identifier for the second partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_struct_sheet_hbond.range_id_1
This data item is a pointer to attribute id in category struct_sheet_range in
the STRUCT_SHEET_RANGE category.
pdbx_struct_sheet_hbond.range_id_2
This data item is a pointer to attribute id in category struct_sheet_range in
the STRUCT_SHEET_RANGE category.
pdbx_struct_sheet_hbond.sheet_id
This data item is a pointer to attribute id in category struct_sheet in the
STRUCT_SHEET category.
pdbx_unobs_or_zero_occ_atoms
Data items in the PDBX_UNOBS_OR_ZERO_OCC_ATOMS category list the
atoms within the entry that are either unobserved or have zero occupancy/
Example 1
<PDBx:pdbx_unobs_or_zero_occ_atomsCategory>
<PDBx:pdbx_unobs_or_zero_occ_atoms id="1">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:PDB_model_num>1</PDBx:PDB_model_num>
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_atom_id>CG</PDBx:auth_atom_id>
<PDBx:auth_comp_id>ARG</PDBx:auth_comp_id>
<PDBx:auth_seq_id>412</PDBx:auth_seq_id>
<PDBx:label_alt_id></PDBx:label_alt_id>
<PDBx:occupancy_flag>1</PDBx:occupancy_flag>
<PDBx:polymer_flag>Y</PDBx:polymer_flag>
</PDBx:pdbx_unobs_or_zero_occ_atoms>
<PDBx:pdbx_unobs_or_zero_occ_atoms id="2">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:PDB_model_num>1</PDBx:PDB_model_num>
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_atom_id>CD</PDBx:auth_atom_id>
<PDBx:auth_comp_id>ARG</PDBx:auth_comp_id>
<PDBx:auth_seq_id>412</PDBx:auth_seq_id>
<PDBx:label_alt_id></PDBx:label_alt_id>
<PDBx:occupancy_flag>1</PDBx:occupancy_flag>
<PDBx:polymer_flag>Y</PDBx:polymer_flag>
</PDBx:pdbx_unobs_or_zero_occ_atoms>
<PDBx:pdbx_unobs_or_zero_occ_atoms id="3">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:PDB_model_num>1</PDBx:PDB_model_num>
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_atom_id>NE</PDBx:auth_atom_id>
<PDBx:auth_comp_id>ARG</PDBx:auth_comp_id>
<PDBx:auth_seq_id>412</PDBx:auth_seq_id>
<PDBx:label_alt_id></PDBx:label_alt_id>
<PDBx:occupancy_flag>1</PDBx:occupancy_flag>
<PDBx:polymer_flag>Y</PDBx:polymer_flag>
</PDBx:pdbx_unobs_or_zero_occ_atoms>
<PDBx:pdbx_unobs_or_zero_occ_atoms id="4">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:PDB_model_num>1</PDBx:PDB_model_num>
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_atom_id>CZ</PDBx:auth_atom_id>
<PDBx:auth_comp_id>ARG</PDBx:auth_comp_id>
<PDBx:auth_seq_id>412</PDBx:auth_seq_id>
<PDBx:label_alt_id></PDBx:label_alt_id>
<PDBx:occupancy_flag>1</PDBx:occupancy_flag>
<PDBx:polymer_flag>Y</PDBx:polymer_flag>
</PDBx:pdbx_unobs_or_zero_occ_atoms>
<PDBx:pdbx_unobs_or_zero_occ_atoms id="5">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:PDB_model_num>1</PDBx:PDB_model_num>
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_atom_id>NH1</PDBx:auth_atom_id>
<PDBx:auth_comp_id>ARG</PDBx:auth_comp_id>
<PDBx:auth_seq_id>412</PDBx:auth_seq_id>
<PDBx:label_alt_id></PDBx:label_alt_id>
<PDBx:occupancy_flag>1</PDBx:occupancy_flag>
<PDBx:polymer_flag>Y</PDBx:polymer_flag>
</PDBx:pdbx_unobs_or_zero_occ_atoms>
<PDBx:pdbx_unobs_or_zero_occ_atoms id="6">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:PDB_model_num>1</PDBx:PDB_model_num>
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_atom_id>NH2</PDBx:auth_atom_id>
<PDBx:auth_comp_id>ARG</PDBx:auth_comp_id>
<PDBx:auth_seq_id>412</PDBx:auth_seq_id>
<PDBx:label_alt_id></PDBx:label_alt_id>
<PDBx:occupancy_flag>1</PDBx:occupancy_flag>
<PDBx:polymer_flag>Y</PDBx:polymer_flag>
</PDBx:pdbx_unobs_or_zero_occ_atoms>
</PDBx:pdbx_unobs_or_zero_occ_atomsCategory>
0
1
1
1
1
1
1
1
1
1
1
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
1
pdbx_unobs_or_zero_occ_atomsCategory
This property indicates that datablock
has a category element pdbx_unobs_or_zero_occ_atoms.
pdbx_unobs_or_zero_occ_atomsItem
Abstract Datatype property for pdbx_unobs_or_zero_occ_atoms items.
reference_to_pdbx_unobs_or_zero_occ_atoms
cross-reference to pdbx_unobs_or_zero_occ_atoms
pdbx_unobs_or_zero_occ_atoms.PDB_ins_code
Part of the identifier for the unobserved or zero occupancy atom.
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the
ATOM_SITE category.
pdbx_unobs_or_zero_occ_atoms.PDB_model_num
Part of the identifier for the unobserved or zero occupancy atom.
This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the
ATOM_SITE category.
pdbx_unobs_or_zero_occ_atoms.auth_asym_id
Part of the identifier for the unobserved or zero occupancy atom.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_unobs_or_zero_occ_atoms.auth_atom_id
Part of the identifier for the unobserved or zero occupancy atom.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
pdbx_unobs_or_zero_occ_atoms.auth_comp_id
Part of the identifier for the unobserved or zero occupancy atom.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_unobs_or_zero_occ_atoms.auth_seq_id
Part of the identifier for the unobserved or zero occupancy atom.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_unobs_or_zero_occ_atoms.label_alt_id
Part of the identifier for the unobserved or zero occupancy atom.
This data item is a pointer to attribute label_alt.id in category atom_site in the
ATOM_SITE category.
pdbx_unobs_or_zero_occ_atoms.label_asym_id
Part of the identifier for the unobserved or zero occupancy atom.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_unobs_or_zero_occ_atoms.label_atom_id
Part of the identifier for the unobserved or zero occupancy atom.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
pdbx_unobs_or_zero_occ_atoms.label_comp_id
Part of the identifier for the unobserved or zero occupancy atom.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_unobs_or_zero_occ_atoms.label_seq_id
Part of the identifier for the unobserved or zero occupancy atom.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
1
0
The value of occupancy flag indicates whether the atom is
either unobserved (=1) or has zero occupancy (=0)
Y
N
The value of polymer flag indicates whether the unobserved or zero
occupancy atom is part of a polymer chain
pdbx_unobs_or_zero_occ_atoms.id
The value of attribute id in category pdbx_unobs_or_zero_occ_atoms must uniquely identify
each item in the PDBX_UNOBS_OR_ZERO_OCC_ATOMS list.
This is an integer serial number.
pdbx_unobs_or_zero_occ_residues
Data items in the PDBX_UNOBS_OR_ZERO_OCC_RESIDUES category list the
residues within the entry that are not observed or have zero occupancy.
Example 1
<PDBx:pdbx_unobs_or_zero_occ_residuesCategory>
<PDBx:pdbx_unobs_or_zero_occ_residues id="1">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:PDB_model_num>1</PDBx:PDB_model_num>
<PDBx:auth_asym_id>B</PDBx:auth_asym_id>
<PDBx:auth_comp_id>VAL</PDBx:auth_comp_id>
<PDBx:auth_seq_id>36</PDBx:auth_seq_id>
<PDBx:occupancy_flag>1</PDBx:occupancy_flag>
<PDBx:polymer_flag>Y</PDBx:polymer_flag>
</PDBx:pdbx_unobs_or_zero_occ_residues>
<PDBx:pdbx_unobs_or_zero_occ_residues id="2">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:PDB_model_num>1</PDBx:PDB_model_num>
<PDBx:auth_asym_id>B</PDBx:auth_asym_id>
<PDBx:auth_comp_id>ARG</PDBx:auth_comp_id>
<PDBx:auth_seq_id>108</PDBx:auth_seq_id>
<PDBx:occupancy_flag>1</PDBx:occupancy_flag>
<PDBx:polymer_flag>Y</PDBx:polymer_flag>
</PDBx:pdbx_unobs_or_zero_occ_residues>
<PDBx:pdbx_unobs_or_zero_occ_residues id="3">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:PDB_model_num>1</PDBx:PDB_model_num>
<PDBx:auth_asym_id>D</PDBx:auth_asym_id>
<PDBx:auth_comp_id>PPI</PDBx:auth_comp_id>
<PDBx:auth_seq_id>438</PDBx:auth_seq_id>
<PDBx:occupancy_flag>1</PDBx:occupancy_flag>
<PDBx:polymer_flag>N</PDBx:polymer_flag>
</PDBx:pdbx_unobs_or_zero_occ_residues>
</PDBx:pdbx_unobs_or_zero_occ_residuesCategory>
0
1
1
1
1
1
1
1
1
1
0
1
0
1
0
1
1
1
1
1
1
pdbx_unobs_or_zero_occ_residuesCategory
This property indicates that datablock
has a category element pdbx_unobs_or_zero_occ_residues.
pdbx_unobs_or_zero_occ_residuesItem
Abstract Datatype property for pdbx_unobs_or_zero_occ_residues items.
reference_to_pdbx_unobs_or_zero_occ_residues
cross-reference to pdbx_unobs_or_zero_occ_residues
pdbx_unobs_or_zero_occ_residues.PDB_ins_code
Part of the identifier for the unobserved or zero occupancy residue.
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the
ATOM_SITE category.
pdbx_unobs_or_zero_occ_residues.PDB_model_num
Part of the identifier for the unobserved or zero occupancy residue.
This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the
ATOM_SITE category.
pdbx_unobs_or_zero_occ_residues.auth_asym_id
Part of the identifier for the unobserved or zero occupancy residue.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_unobs_or_zero_occ_residues.auth_comp_id
Part of the identifier for the unobserved or zero occupancy residue.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_unobs_or_zero_occ_residues.auth_seq_id
Part of the identifier for the unobserved or zero occupancy residue.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_unobs_or_zero_occ_residues.label_asym_id
Part of the identifier for the unobserved or zero occupancy residue.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_unobs_or_zero_occ_residues.label_comp_id
Part of the identifier for the unobserved or zero occupancy residue.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_unobs_or_zero_occ_residues.label_seq_id
Part of the identifier for the unobserved or zero occupancy residue.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
1
0
The value of occupancy flag indicates whether the residue
is unobserved (= 1) or the coordinates have an occupancy of zero (=0)
Y
N
The value of polymer flag indicates whether the unobserved or
zero occupancy residue is part of a polymer chain or not
pdbx_unobs_or_zero_occ_residues.id
The value of attribute id in category pdbx_unobs_or_zero_occ_residues must uniquely identify
each item in the PDBX_UNOBS_OR_ZERO_OCC_RESIDUES list.
This is an integer serial number.
pdbx_validate_chiral
Data items in the PDBX_VALIDATE_CHIRAL category list the
residues that contain unexpected configuration of chiral
centers.
IMPROPER HA N C CB chirality CA
IMPROPER HB1 HB2 CA CG stereo CB
as this number approaches (+) or (-) 180.0, then the
error in predicting the true chirality of the center increases.
Improper dihedrals are a measure of the chirality/planarity of the
structure at a specific atom. Values around -35 or +35 are expected
for chiral atoms, and values around 0 for planar atoms.
HERE improper C---N----CA---CB done
expected answer is around -120 mean -122.52
D-amino acid is +120.0
Example 1
<PDBx:pdbx_validate_chiralCategory>
<PDBx:pdbx_validate_chiral id="1">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:PDB_model_num>0</PDBx:PDB_model_num>
<PDBx:auth_asym_id>ASP</PDBx:auth_asym_id>
<PDBx:auth_comp_id>B</PDBx:auth_comp_id>
<PDBx:auth_seq_id>405</PDBx:auth_seq_id>
<PDBx:details>ALPHA-CARBON</PDBx:details>
<PDBx:omega>150.48</PDBx:omega>
</PDBx:pdbx_validate_chiral>
</PDBx:pdbx_validate_chiralCategory>
0
1
1
1
1
1
1
1
1
1
0
1
1
1
1
pdbx_validate_chiralCategory
This property indicates that datablock
has a category element pdbx_validate_chiral.
pdbx_validate_chiralItem
Abstract Datatype property for pdbx_validate_chiral items.
reference_to_pdbx_validate_chiral
cross-reference to pdbx_validate_chiral
pdbx_validate_chiral.PDB_ins_code
Optional identifier of the residue
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the
ATOM_SITE category.
pdbx_validate_chiral.PDB_model_num
The model number for the given residue
This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the
ATOM_SITE category.
pdbx_validate_chiral.auth_asym_id
Part of the identifier of the residue
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_chiral.auth_comp_id
Part of the identifier of the residue
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_chiral.auth_seq_id
Part of the identifier of the residue
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_chiral.details
A description of the outlier angle e.g. ALPHA-CARBON
pdbx_validate_chiral.omega
The value of the OMEGA angle for the peptide linkage between
the two defined residues
pdbx_validate_chiral.id
The value of attribute id in category pdbx_validate_chiral must
uniquely identify each item in the PDBX_VALIDATE_CHIRAL list.
This is an integer serial number.
pdbx_validate_close_contact
Data items in the PDBX_VALIDATE_CLOSE_CONTACT category list the
atoms within the entry that are in close contact with regard
the distances expected from either covalent bonding or closest
approach by van der Waals contacts. Contacts within
the asymmetric unit are considered.
For those contacts not involving hydrogen a limit of
2.2 Angstroms is used. For contacts involving a hydrogen atom
a cutoff of 1.6 Angstroms is used.
Example 1
<PDBx:pdbx_validate_close_contactCategory>
<PDBx:pdbx_validate_close_contact id="1">
<PDBx:PDB_ins_code_1></PDBx:PDB_ins_code_1>
<PDBx:PDB_ins_code_2></PDBx:PDB_ins_code_2>
<PDBx:PDB_model_num>1</PDBx:PDB_model_num>
<PDBx:auth_asym_id_1>B</PDBx:auth_asym_id_1>
<PDBx:auth_asym_id_2>B</PDBx:auth_asym_id_2>
<PDBx:auth_atom_id_1></PDBx:auth_atom_id_1>
<PDBx:auth_atom_id_2></PDBx:auth_atom_id_2>
<PDBx:auth_comp_id_1>VAL</PDBx:auth_comp_id_1>
<PDBx:auth_comp_id_2>ARG</PDBx:auth_comp_id_2>
<PDBx:auth_seq_id_1>36</PDBx:auth_seq_id_1>
<PDBx:auth_seq_id_2>108</PDBx:auth_seq_id_2>
<PDBx:dist>2.16</PDBx:dist>
<PDBx:label_alt_id_1></PDBx:label_alt_id_1>
<PDBx:label_alt_id_2></PDBx:label_alt_id_2>
</PDBx:pdbx_validate_close_contact>
<PDBx:pdbx_validate_close_contact id="2">
<PDBx:PDB_ins_code_1></PDBx:PDB_ins_code_1>
<PDBx:PDB_ins_code_2></PDBx:PDB_ins_code_2>
<PDBx:PDB_model_num>1</PDBx:PDB_model_num>
<PDBx:auth_asym_id_1>B</PDBx:auth_asym_id_1>
<PDBx:auth_asym_id_2>B</PDBx:auth_asym_id_2>
<PDBx:auth_atom_id_1></PDBx:auth_atom_id_1>
<PDBx:auth_atom_id_2></PDBx:auth_atom_id_2>
<PDBx:auth_comp_id_1>ARG</PDBx:auth_comp_id_1>
<PDBx:auth_comp_id_2>VAL</PDBx:auth_comp_id_2>
<PDBx:auth_seq_id_1>108</PDBx:auth_seq_id_1>
<PDBx:auth_seq_id_2>36</PDBx:auth_seq_id_2>
<PDBx:dist>2.16</PDBx:dist>
<PDBx:label_alt_id_1></PDBx:label_alt_id_1>
<PDBx:label_alt_id_2></PDBx:label_alt_id_2>
</PDBx:pdbx_validate_close_contact>
</PDBx:pdbx_validate_close_contactCategory>
0
1
0
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
0
1
0
1
0
1
0
1
1
pdbx_validate_close_contactCategory
This property indicates that datablock
has a category element pdbx_validate_close_contact.
pdbx_validate_close_contactItem
Abstract Datatype property for pdbx_validate_close_contact items.
reference_to_pdbx_validate_close_contact
cross-reference to pdbx_validate_close_contact
pdbx_validate_close_contact.PDB_ins_code_1
Optional identifier of the first of the two atom sites that
define the close contact.
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the
ATOM_SITE category.
pdbx_validate_close_contact.PDB_ins_code_2
Optional identifier of the second of the two atom sites that
define the close contact.
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the
ATOM_SITE category.
pdbx_validate_close_contact.PDB_model_num
The model number for the given angle
pdbx_validate_close_contact.auth_asym_id_1
Part of the identifier of the first of the two atom sites that
define the close contact.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_close_contact.auth_asym_id_2
Part of the identifier of the second of the two atom sites
that define the close contact.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_close_contact.auth_atom_id_1
Part of the identifier of the first of the two atom sites that
define the close contact.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_close_contact.auth_atom_id_2
Part of the identifier of the second of the two atom sites
that define the close contact.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_close_contact.auth_comp_id_1
Part of the identifier of the first of the two atom sites that
define the close contact.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_close_contact.auth_comp_id_2
Part of the identifier of the second of the two atom sites
that define the close contact.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_close_contact.auth_seq_id_1
Part of the identifier of the first of the two atom sites that
define the close contact.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_close_contact.auth_seq_id_2
Part of the identifier of the second of the two atom sites
that define the close contact.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_close_contact.dist
The value of the close contact for the two atoms defined.
pdbx_validate_close_contact.label_alt_id_1
An optional identifier of the first of the two atoms that
define the close contact.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_close_contact.label_alt_id_2
An optional identifier of the second of the two atoms that
define the close contact.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_close_contact.symm_as_xyz_1
The symmetry of the first of the two atoms define the close contact.
The Symmetry equivalent position is given in the 'xyz' representation.
pdbx_validate_close_contact.symm_as_xyz_2
The symmetry of the second of the two atoms define the close contact.
The Symmetry equivalent position is given in the 'xyz' representation.
pdbx_validate_close_contact.id
The value of attribute id in category pdbx_validate_close_contact must uniquely identify
each item in the PDBX_VALIDATE_CLOSE_CONTACT list.
This is an integer serial number.
pdbx_validate_main_chain_plane
Data items in the PDBX_VALIDATE_MAIN_CHAIN_PLANE category list the
residues that contain unexpected deviations from planes
for main chain atoms as defined by the improper torsion
angle describing planarity:
PLANARITY = C(i-1) - CA(i-1) - N(i) - O(i-1) ==> planar < 5
as a pseudo torsion
Example 1
<PDBx:pdbx_validate_main_chain_planeCategory>
<PDBx:pdbx_validate_main_chain_plane id="1">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:PDB_model_num>0</PDBx:PDB_model_num>
<PDBx:auth_asym_id>G</PDBx:auth_asym_id>
<PDBx:auth_comp_id>TRP</PDBx:auth_comp_id>
<PDBx:auth_seq_id>20</PDBx:auth_seq_id>
<PDBx:improper_torsion_angle>29.901</PDBx:improper_torsion_angle>
</PDBx:pdbx_validate_main_chain_plane>
<PDBx:pdbx_validate_main_chain_plane id="2">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:PDB_model_num>0</PDBx:PDB_model_num>
<PDBx:auth_asym_id>G</PDBx:auth_asym_id>
<PDBx:auth_comp_id>TRP</PDBx:auth_comp_id>
<PDBx:auth_seq_id>21</PDBx:auth_seq_id>
<PDBx:improper_torsion_angle>-42.450</PDBx:improper_torsion_angle>
</PDBx:pdbx_validate_main_chain_plane>
</PDBx:pdbx_validate_main_chain_planeCategory>
0
1
1
1
1
1
1
1
1
1
1
1
1
pdbx_validate_main_chain_planeCategory
This property indicates that datablock
has a category element pdbx_validate_main_chain_plane.
pdbx_validate_main_chain_planeItem
Abstract Datatype property for pdbx_validate_main_chain_plane items.
reference_to_pdbx_validate_main_chain_plane
cross-reference to pdbx_validate_main_chain_plane
pdbx_validate_main_chain_plane.PDB_ins_code
Optional identifier of the residue in which the plane is calculated
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the
ATOM_SITE category.
pdbx_validate_main_chain_plane.PDB_model_num
The model number for the residue in which the plane is calculated
This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the
ATOM_SITE category.
pdbx_validate_main_chain_plane.auth_asym_id
Part of the identifier of the residue in which the plane is calculated
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_main_chain_plane.auth_comp_id
Part of the identifier of the residue in which the plane is calculated
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_main_chain_plane.auth_seq_id
Part of the identifier of the residue in which the plane is calculated
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_main_chain_plane.improper_torsion_angle
The value for the torsion angle C(i-1) - CA(i-1) - N(i) - O(i-1)
pdbx_validate_main_chain_plane.id
The value of attribute id in category pdbx_validate_main_chain_plane must uniquely identify
each item in the PDBX_VALIDATE_MAIN_CHAIN_PLANE list.
This is an integer serial number.
pdbx_validate_peptide_omega
Data items in the PDBX_VALIDATE_PEPTIDE_OMEGA category list the
residues that contain peptide bonds deviate
significantly from both cis and trans conformation.
cis bonds, if any, are listed on cispep records.
trans is defined as 180 +/- 30 and
cis is defined as 0 +/- 30 degrees.
Example 1
<PDBx:pdbx_validate_peptide_omegaCategory>
<PDBx:pdbx_validate_peptide_omega id="1">
<PDBx:PDB_ins_code_1></PDBx:PDB_ins_code_1>
<PDBx:PDB_ins_code_2></PDBx:PDB_ins_code_2>
<PDBx:PDB_model_num>0</PDBx:PDB_model_num>
<PDBx:auth_asym_id_1>ASP</PDBx:auth_asym_id_1>
<PDBx:auth_asym_id_2>ARG</PDBx:auth_asym_id_2>
<PDBx:auth_comp_id_1>A</PDBx:auth_comp_id_1>
<PDBx:auth_comp_id_2>A</PDBx:auth_comp_id_2>
<PDBx:auth_seq_id_1>414</PDBx:auth_seq_id_1>
<PDBx:auth_seq_id_2>413</PDBx:auth_seq_id_2>
<PDBx:label_alt_id_1></PDBx:label_alt_id_1>
<PDBx:label_alt_id_2></PDBx:label_alt_id_2>
<PDBx:omega>147.84</PDBx:omega>
</PDBx:pdbx_validate_peptide_omega>
<PDBx:pdbx_validate_peptide_omega id="2">
<PDBx:PDB_ins_code_1></PDBx:PDB_ins_code_1>
<PDBx:PDB_ins_code_2></PDBx:PDB_ins_code_2>
<PDBx:PDB_model_num>0</PDBx:PDB_model_num>
<PDBx:auth_asym_id_1>ASN</PDBx:auth_asym_id_1>
<PDBx:auth_asym_id_2>ALA</PDBx:auth_asym_id_2>
<PDBx:auth_comp_id_1>B</PDBx:auth_comp_id_1>
<PDBx:auth_comp_id_2>B</PDBx:auth_comp_id_2>
<PDBx:auth_seq_id_1>289</PDBx:auth_seq_id_1>
<PDBx:auth_seq_id_2>288</PDBx:auth_seq_id_2>
<PDBx:label_alt_id_1></PDBx:label_alt_id_1>
<PDBx:label_alt_id_2></PDBx:label_alt_id_2>
<PDBx:omega>-39.12</PDBx:omega>
</PDBx:pdbx_validate_peptide_omega>
</PDBx:pdbx_validate_peptide_omegaCategory>
0
1
0
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
0
1
0
1
1
1
1
pdbx_validate_peptide_omegaCategory
This property indicates that datablock
has a category element pdbx_validate_peptide_omega.
pdbx_validate_peptide_omegaItem
Abstract Datatype property for pdbx_validate_peptide_omega items.
reference_to_pdbx_validate_peptide_omega
cross-reference to pdbx_validate_peptide_omega
pdbx_validate_peptide_omega.PDB_ins_code_1
Optional identifier of the first residue in the bond
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the
ATOM_SITE category.
pdbx_validate_peptide_omega.PDB_ins_code_2
Optional identifier of the second residue in the bond
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the
ATOM_SITE category.
pdbx_validate_peptide_omega.PDB_model_num
The model number for the given residue
This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the
ATOM_SITE category.
pdbx_validate_peptide_omega.auth_asym_id_1
Part of the identifier of the first residue in the bond
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_peptide_omega.auth_asym_id_2
Part of the identifier of the second residue in the bond
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_peptide_omega.auth_comp_id_1
Part of the identifier of the first residue in the bond
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_peptide_omega.auth_comp_id_2
Part of the identifier of the second residue in the bond
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_peptide_omega.auth_seq_id_1
Part of the identifier of the first residue in the bond
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_peptide_omega.auth_seq_id_2
Part of the identifier of the second residue in the bond
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_peptide_omega.label_alt_id_1
Optional identifier of the first residue in the torsion angle
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_peptide_omega.label_alt_id_2
Optional identifier of the second residue in the torsion angle
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_peptide_omega.omega
The value of the OMEGA angle for the peptide linkage between
the two defined residues
pdbx_validate_peptide_omega.id
The value of attribute id in category pdbx_validate_peptide_omega must
uniquely identify each item in the PDBX_VALIDATE_PEPTIDE_OMEGA list.
This is an integer serial number.
pdbx_validate_planes
Data items in the PDBX_VALIDATE_PLANES category list the
residues that contain unexpected deviations from planes
centers.
Example 1
<PDBx:pdbx_validate_planesCategory>
<PDBx:pdbx_validate_planes id="1">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:PDB_model_num>1</PDBx:PDB_model_num>
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_comp_id>DG</PDBx:auth_comp_id>
<PDBx:auth_seq_id>3</PDBx:auth_seq_id>
<PDBx:rmsd>0.068</PDBx:rmsd>
<PDBx:type>SIDE CHAIN</PDBx:type>
</PDBx:pdbx_validate_planes>
<PDBx:pdbx_validate_planes id="2">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:PDB_model_num>1</PDBx:PDB_model_num>
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_comp_id>DT</PDBx:auth_comp_id>
<PDBx:auth_seq_id>4</PDBx:auth_seq_id>
<PDBx:rmsd>0.198</PDBx:rmsd>
<PDBx:type>SIDE CHAIN</PDBx:type>
</PDBx:pdbx_validate_planes>
<PDBx:pdbx_validate_planes id="3">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:PDB_model_num>1</PDBx:PDB_model_num>
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_comp_id>DC</PDBx:auth_comp_id>
<PDBx:auth_seq_id>8</PDBx:auth_seq_id>
<PDBx:rmsd>0.090</PDBx:rmsd>
<PDBx:type>SIDE CHAIN</PDBx:type>
</PDBx:pdbx_validate_planes>
</PDBx:pdbx_validate_planesCategory>
0
1
1
1
1
1
1
1
1
1
1
1
1
1
1
pdbx_validate_planesCategory
This property indicates that datablock
has a category element pdbx_validate_planes.
pdbx_validate_planesItem
Abstract Datatype property for pdbx_validate_planes items.
reference_to_pdbx_validate_planes
cross-reference to pdbx_validate_planes
pdbx_validate_planes.PDB_ins_code
Optional identifier of the residue in which the plane is calculated
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the
ATOM_SITE category.
pdbx_validate_planes.PDB_model_num
The model number for the given angle
This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the
ATOM_SITE category.
pdbx_validate_planes.auth_asym_id
Part of the identifier of the residue in which the plane is calculated
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_planes.auth_comp_id
Part of the identifier of the residue in which the plane is calculated
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_planes.auth_seq_id
Part of the identifier of the residue in which the plane is calculated
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_planes.rmsd
The value of the overall deviation from ideal plane for the atoms
defining the plane.
MAIN_CHAIN
SIDE_CHAIN
MAIN CHAIN
SIDE CHAIN
The type of plane - MAIN CHAIN or SIDE CHAIN atoms
pdbx_validate_planes.id
The value of attribute id in category pdbx_validate_planes must uniquely identify
each item in the PDBX_VALIDATE_PLANES list.
This is an integer serial number.
pdbx_validate_planes_atom
Data items in the PDBX_VALIDATE_PLANES_ATOM category list the
residues that contain unexpected deviations from planes
centers.
Example 1
<PDBx:pdbx_validate_planes_atomCategory>
<PDBx:pdbx_validate_planes_atom id="1">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:PDB_model_num>1</PDBx:PDB_model_num>
<PDBx:atom_deviation>0.003</PDBx:atom_deviation>
<PDBx:auth_asym_id>DG</PDBx:auth_asym_id>
<PDBx:auth_atom_id>N1</PDBx:auth_atom_id>
<PDBx:auth_comp_id>A</PDBx:auth_comp_id>
<PDBx:auth_seq_id>3</PDBx:auth_seq_id>
<PDBx:plane_id>1</PDBx:plane_id>
</PDBx:pdbx_validate_planes_atom>
<PDBx:pdbx_validate_planes_atom id="2">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:PDB_model_num>1</PDBx:PDB_model_num>
<PDBx:atom_deviation>0.011</PDBx:atom_deviation>
<PDBx:auth_asym_id>DG</PDBx:auth_asym_id>
<PDBx:auth_atom_id>C2</PDBx:auth_atom_id>
<PDBx:auth_comp_id>A</PDBx:auth_comp_id>
<PDBx:auth_seq_id>3</PDBx:auth_seq_id>
<PDBx:plane_id>1</PDBx:plane_id>
</PDBx:pdbx_validate_planes_atom>
<PDBx:pdbx_validate_planes_atom id="3">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:PDB_model_num>1</PDBx:PDB_model_num>
<PDBx:atom_deviation>0.074</PDBx:atom_deviation>
<PDBx:auth_asym_id>DG</PDBx:auth_asym_id>
<PDBx:auth_atom_id>N2</PDBx:auth_atom_id>
<PDBx:auth_comp_id>A</PDBx:auth_comp_id>
<PDBx:auth_seq_id>3</PDBx:auth_seq_id>
<PDBx:plane_id>1</PDBx:plane_id>
</PDBx:pdbx_validate_planes_atom>
<PDBx:pdbx_validate_planes_atom id="4">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:PDB_model_num>1</PDBx:PDB_model_num>
<PDBx:atom_deviation>0.005</PDBx:atom_deviation>
<PDBx:auth_asym_id>DG</PDBx:auth_asym_id>
<PDBx:auth_atom_id>N3</PDBx:auth_atom_id>
<PDBx:auth_comp_id>A</PDBx:auth_comp_id>
<PDBx:auth_seq_id>3</PDBx:auth_seq_id>
<PDBx:plane_id>1</PDBx:plane_id>
</PDBx:pdbx_validate_planes_atom>
<PDBx:pdbx_validate_planes_atom id="5">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:PDB_model_num>1</PDBx:PDB_model_num>
<PDBx:atom_deviation>0.010</PDBx:atom_deviation>
<PDBx:auth_asym_id>DG</PDBx:auth_asym_id>
<PDBx:auth_atom_id>C4</PDBx:auth_atom_id>
<PDBx:auth_comp_id>A</PDBx:auth_comp_id>
<PDBx:auth_seq_id>3</PDBx:auth_seq_id>
<PDBx:plane_id>1</PDBx:plane_id>
</PDBx:pdbx_validate_planes_atom>
<PDBx:pdbx_validate_planes_atom id="6">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:PDB_model_num>1</PDBx:PDB_model_num>
<PDBx:atom_deviation>0.029</PDBx:atom_deviation>
<PDBx:auth_asym_id>DG</PDBx:auth_asym_id>
<PDBx:auth_atom_id>C5</PDBx:auth_atom_id>
<PDBx:auth_comp_id>A</PDBx:auth_comp_id>
<PDBx:auth_seq_id>3</PDBx:auth_seq_id>
<PDBx:plane_id>1</PDBx:plane_id>
</PDBx:pdbx_validate_planes_atom>
<PDBx:pdbx_validate_planes_atom id="7">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:PDB_model_num>1</PDBx:PDB_model_num>
<PDBx:atom_deviation>0.039</PDBx:atom_deviation>
<PDBx:auth_asym_id>DG</PDBx:auth_asym_id>
<PDBx:auth_atom_id>C6</PDBx:auth_atom_id>
<PDBx:auth_comp_id>A</PDBx:auth_comp_id>
<PDBx:auth_seq_id>3</PDBx:auth_seq_id>
<PDBx:plane_id>1</PDBx:plane_id>
</PDBx:pdbx_validate_planes_atom>
<PDBx:pdbx_validate_planes_atom id="8">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:PDB_model_num>1</PDBx:PDB_model_num>
<PDBx:atom_deviation>0.074</PDBx:atom_deviation>
<PDBx:auth_asym_id>DG</PDBx:auth_asym_id>
<PDBx:auth_atom_id>O6</PDBx:auth_atom_id>
<PDBx:auth_comp_id>A</PDBx:auth_comp_id>
<PDBx:auth_seq_id>3</PDBx:auth_seq_id>
<PDBx:plane_id>1</PDBx:plane_id>
</PDBx:pdbx_validate_planes_atom>
<PDBx:pdbx_validate_planes_atom id="9">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:PDB_model_num>1</PDBx:PDB_model_num>
<PDBx:atom_deviation>0.050</PDBx:atom_deviation>
<PDBx:auth_asym_id>DG</PDBx:auth_asym_id>
<PDBx:auth_atom_id>N7</PDBx:auth_atom_id>
<PDBx:auth_comp_id>A</PDBx:auth_comp_id>
<PDBx:auth_seq_id>3</PDBx:auth_seq_id>
<PDBx:plane_id>1</PDBx:plane_id>
</PDBx:pdbx_validate_planes_atom>
<PDBx:pdbx_validate_planes_atom id="10">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:PDB_model_num>1</PDBx:PDB_model_num>
<PDBx:atom_deviation>0.129</PDBx:atom_deviation>
<PDBx:auth_asym_id>DG</PDBx:auth_asym_id>
<PDBx:auth_atom_id>C8</PDBx:auth_atom_id>
<PDBx:auth_comp_id>A</PDBx:auth_comp_id>
<PDBx:auth_seq_id>3</PDBx:auth_seq_id>
<PDBx:plane_id>1</PDBx:plane_id>
</PDBx:pdbx_validate_planes_atom>
<PDBx:pdbx_validate_planes_atom id="11">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:PDB_model_num>1</PDBx:PDB_model_num>
<PDBx:atom_deviation>0.033</PDBx:atom_deviation>
<PDBx:auth_asym_id>DG</PDBx:auth_asym_id>
<PDBx:auth_atom_id>N9</PDBx:auth_atom_id>
<PDBx:auth_comp_id>A</PDBx:auth_comp_id>
<PDBx:auth_seq_id>3</PDBx:auth_seq_id>
<PDBx:plane_id>1</PDBx:plane_id>
</PDBx:pdbx_validate_planes_atom>
<PDBx:pdbx_validate_planes_atom id="12">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:PDB_model_num>1</PDBx:PDB_model_num>
<PDBx:atom_deviation>0.147</PDBx:atom_deviation>
<PDBx:auth_asym_id>DG</PDBx:auth_asym_id>
<PDBx:auth_atom_id>C1'</PDBx:auth_atom_id>
<PDBx:auth_comp_id>A</PDBx:auth_comp_id>
<PDBx:auth_seq_id>3</PDBx:auth_seq_id>
<PDBx:plane_id>1</PDBx:plane_id>
</PDBx:pdbx_validate_planes_atom>
<PDBx:pdbx_validate_planes_atom id="1">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:PDB_model_num>1</PDBx:PDB_model_num>
<PDBx:atom_deviation>0.069</PDBx:atom_deviation>
<PDBx:auth_asym_id>DT</PDBx:auth_asym_id>
<PDBx:auth_atom_id>N1</PDBx:auth_atom_id>
<PDBx:auth_comp_id>A</PDBx:auth_comp_id>
<PDBx:auth_seq_id>4</PDBx:auth_seq_id>
<PDBx:plane_id>2</PDBx:plane_id>
</PDBx:pdbx_validate_planes_atom>
</PDBx:pdbx_validate_planes_atomCategory>
0
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
pdbx_validate_planes_atomCategory
This property indicates that datablock
has a category element pdbx_validate_planes_atom.
pdbx_validate_planes_atomItem
Abstract Datatype property for pdbx_validate_planes_atom items.
reference_to_pdbx_validate_planes_atom
cross-reference to pdbx_validate_planes_atom
pdbx_validate_planes_atom.PDB_ins_code
Optional identifier of an atom site that defines the plane
pdbx_validate_planes_atom.PDB_model_num
The model number for an atom site defining the plane
This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the
ATOM_SITE category.
pdbx_validate_planes_atom.atom_deviation
The deviation from the plane per atom
pdbx_validate_planes_atom.auth_asym_id
Part of the identifier of an atom site that defines the plane
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_planes_atom.auth_atom_id
Part of the identifier of an atom site that defines the plane
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_planes_atom.auth_comp_id
Part of the identifier of an atom site that defines the plane
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_planes_atom.auth_seq_id
Part of the identifier of an atom site that defines the plane
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_planes_atom.plane_id
A pointer to attribute id
in category pdbx_validate_planes This is an integer serial number.
pdbx_validate_planes_atom.id
The value of attribute id in category pdbx_validate_planes_atom must uniquely identify
each item in the PDBX_VALIDATE_PLANES_ATOM list.
This is an integer serial number.
pdbx_validate_rmsd_angle
Data items in the PDBX_VALIDATE_RMSD_ANGLE category list the
the covalent bond angles found in an entry that have
values which deviate from expected values by more
than 6*rmsd for the particular entry from the expected standard
value
Example 1
<PDBx:pdbx_validate_rmsd_angleCategory>
<PDBx:pdbx_validate_rmsd_angle id="1">
<PDBx:PDB_ins_code_1></PDBx:PDB_ins_code_1>
<PDBx:PDB_ins_code_2></PDBx:PDB_ins_code_2>
<PDBx:PDB_ins_code_3></PDBx:PDB_ins_code_3>
<PDBx:PDB_model_num>0</PDBx:PDB_model_num>
<PDBx:angle_deviation>-3.14</PDBx:angle_deviation>
<PDBx:angle_value>117.16</PDBx:angle_value>
<PDBx:auth_asym_id_1>A</PDBx:auth_asym_id_1>
<PDBx:auth_asym_id_2>A</PDBx:auth_asym_id_2>
<PDBx:auth_asym_id_3>A</PDBx:auth_asym_id_3>
<PDBx:auth_atom_id_1>NE</PDBx:auth_atom_id_1>
<PDBx:auth_atom_id_2>CZ</PDBx:auth_atom_id_2>
<PDBx:auth_atom_id_3>NH2</PDBx:auth_atom_id_3>
<PDBx:auth_comp_id_1>ARG</PDBx:auth_comp_id_1>
<PDBx:auth_comp_id_2>ARG</PDBx:auth_comp_id_2>
<PDBx:auth_comp_id_3>ARG</PDBx:auth_comp_id_3>
<PDBx:auth_seq_id_1>35</PDBx:auth_seq_id_1>
<PDBx:auth_seq_id_2>35</PDBx:auth_seq_id_2>
<PDBx:auth_seq_id_3>35</PDBx:auth_seq_id_3>
<PDBx:label_alt_id_1></PDBx:label_alt_id_1>
<PDBx:label_alt_id_2></PDBx:label_alt_id_2>
<PDBx:label_alt_id_3></PDBx:label_alt_id_3>
<PDBx:linker_flag>N</PDBx:linker_flag>
</PDBx:pdbx_validate_rmsd_angle>
<PDBx:pdbx_validate_rmsd_angle id="2">
<PDBx:PDB_ins_code_1></PDBx:PDB_ins_code_1>
<PDBx:PDB_ins_code_2></PDBx:PDB_ins_code_2>
<PDBx:PDB_ins_code_3></PDBx:PDB_ins_code_3>
<PDBx:PDB_model_num>0</PDBx:PDB_model_num>
<PDBx:angle_deviation>34.68</PDBx:angle_deviation>
<PDBx:angle_value>148.88</PDBx:angle_value>
<PDBx:auth_asym_id_1>A</PDBx:auth_asym_id_1>
<PDBx:auth_asym_id_2>A</PDBx:auth_asym_id_2>
<PDBx:auth_asym_id_3>A</PDBx:auth_asym_id_3>
<PDBx:auth_atom_id_1>CB</PDBx:auth_atom_id_1>
<PDBx:auth_atom_id_2>CG</PDBx:auth_atom_id_2>
<PDBx:auth_atom_id_3>CD</PDBx:auth_atom_id_3>
<PDBx:auth_comp_id_1>GLU</PDBx:auth_comp_id_1>
<PDBx:auth_comp_id_2>GLU</PDBx:auth_comp_id_2>
<PDBx:auth_comp_id_3>GLU</PDBx:auth_comp_id_3>
<PDBx:auth_seq_id_1>166</PDBx:auth_seq_id_1>
<PDBx:auth_seq_id_2>166</PDBx:auth_seq_id_2>
<PDBx:auth_seq_id_3>166</PDBx:auth_seq_id_3>
<PDBx:label_alt_id_1></PDBx:label_alt_id_1>
<PDBx:label_alt_id_2></PDBx:label_alt_id_2>
<PDBx:label_alt_id_3></PDBx:label_alt_id_3>
<PDBx:linker_flag>N</PDBx:linker_flag>
</PDBx:pdbx_validate_rmsd_angle>
</PDBx:pdbx_validate_rmsd_angleCategory>
0
1
0
1
0
1
1
1
1
1
0
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
0
1
0
1
0
1
0
1
1
pdbx_validate_rmsd_angleCategory
This property indicates that datablock
has a category element pdbx_validate_rmsd_angle.
pdbx_validate_rmsd_angleItem
Abstract Datatype property for pdbx_validate_rmsd_angle items.
reference_to_pdbx_validate_rmsd_angle
cross-reference to pdbx_validate_rmsd_angle
pdbx_validate_rmsd_angle.PDB_ins_code_1
Optional identifier of the first of the three atom sites that
define the angle.
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the
ATOM_SITE category.
pdbx_validate_rmsd_angle.PDB_ins_code_2
Optional identifier of the second of the three atom sites that
define the angle.
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the
ATOM_SITE category.
pdbx_validate_rmsd_angle.PDB_ins_code_3
Optional identifier of the third of the three atom sites that
define the angle.
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the
ATOM_SITE category.
pdbx_validate_rmsd_angle.PDB_model_num
The model number for the given angle
pdbx_validate_rmsd_angle.angle_deviation
Value of the deviation (in degrees) from 6*REBI for the angle bounded
by the three sites from the expected dictionary value.
pdbx_validate_rmsd_angle.angle_value
The value of the bond angle
pdbx_validate_rmsd_angle.auth_asym_id_1
Part of the identifier of the first of the three atom sites that
define the angle.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_rmsd_angle.auth_asym_id_2
identifier of the second of the three atom sites
that define the angle.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_rmsd_angle.auth_asym_id_3
Part of the identifier of the third of the three atom sites that
define the angle.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_rmsd_angle.auth_atom_id_1
Part of the identifier of the first of the three atom sites that
define the angle.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_rmsd_angle.auth_atom_id_2
Part of the identifier of the second of the three atom sites
that define the angle.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_rmsd_angle.auth_atom_id_3
Part of the identifier of the third of the three atom sites that
define the angle.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_rmsd_angle.auth_comp_id_1
Part of the identifier of the first of the three atom sites that
define the angle.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_rmsd_angle.auth_comp_id_2
Part of the identifier of the second of the three atom sites
that define the angle.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_rmsd_angle.auth_comp_id_3
Part of the identifier of the third of the three atom sites that
define the angle.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_rmsd_angle.auth_seq_id_1
Part of the identifier of the first of the three atom sites that
define the angle.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_rmsd_angle.auth_seq_id_2
Part of the identifier of the second of the three atom sites
that define the angle.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_rmsd_angle.auth_seq_id_3
Part of the identifier of the third of the three atom sites that
define the angle.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_rmsd_angle.label_alt_id_1
An optional identifier of the first of the three atoms that
define the covalent angle.
This data item is a pointer to attribute label_alt.id in category atom_site in the
ATOM_SITE category.
pdbx_validate_rmsd_angle.label_alt_id_2
An optional identifier of the second of the three atoms that
define the covalent angle.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_rmsd_angle.label_alt_id_3
An optional identifier of the third of the three atoms that
define the covalent angle.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_rmsd_angle.linker_flag
A flag to indicate if the angle is between two residues
pdbx_validate_rmsd_angle.id
The value of attribute id in category pdbx_validate_rmsd_angle must uniquely identify
each item in the PDBX_VALIDATE_RMSD_ANGLE list.
This is an integer serial number.
pdbx_validate_rmsd_bond
Data items in the PDBX_VALIDATE_RMSD_BOND category list the
covalent bonds that have values which deviate from expected
values by more than 6*rmsd.
Example 1
<PDBx:pdbx_validate_rmsd_bondCategory>
<PDBx:pdbx_validate_rmsd_bond id="1">
<PDBx:PDB_ins_code_1></PDBx:PDB_ins_code_1>
<PDBx:PDB_ins_code_2></PDBx:PDB_ins_code_2>
<PDBx:PDB_model_num>0</PDBx:PDB_model_num>
<PDBx:auth_asym_id_1>A</PDBx:auth_asym_id_1>
<PDBx:auth_asym_id_2>A</PDBx:auth_asym_id_2>
<PDBx:auth_atom_id_1>CD</PDBx:auth_atom_id_1>
<PDBx:auth_atom_id_2>CE</PDBx:auth_atom_id_2>
<PDBx:auth_comp_id_1>LYS</PDBx:auth_comp_id_1>
<PDBx:auth_comp_id_2>LYS</PDBx:auth_comp_id_2>
<PDBx:auth_seq_id_1>152</PDBx:auth_seq_id_1>
<PDBx:auth_seq_id_2>152</PDBx:auth_seq_id_2>
<PDBx:bond_deviation>-0.372</PDBx:bond_deviation>
<PDBx:bond_value>1.136</PDBx:bond_value>
<PDBx:label_alt_id_1></PDBx:label_alt_id_1>
<PDBx:label_alt_id_2></PDBx:label_alt_id_2>
<PDBx:linker_flag>N</PDBx:linker_flag>
</PDBx:pdbx_validate_rmsd_bond>
<PDBx:pdbx_validate_rmsd_bond id="2">
<PDBx:PDB_ins_code_1></PDBx:PDB_ins_code_1>
<PDBx:PDB_ins_code_2></PDBx:PDB_ins_code_2>
<PDBx:PDB_model_num>0</PDBx:PDB_model_num>
<PDBx:auth_asym_id_1>A</PDBx:auth_asym_id_1>
<PDBx:auth_asym_id_2>A</PDBx:auth_asym_id_2>
<PDBx:auth_atom_id_1>CG</PDBx:auth_atom_id_1>
<PDBx:auth_atom_id_2>CD</PDBx:auth_atom_id_2>
<PDBx:auth_comp_id_1>GLU</PDBx:auth_comp_id_1>
<PDBx:auth_comp_id_2>GLU</PDBx:auth_comp_id_2>
<PDBx:auth_seq_id_1>166</PDBx:auth_seq_id_1>
<PDBx:auth_seq_id_2>166</PDBx:auth_seq_id_2>
<PDBx:bond_deviation>-0.622</PDBx:bond_deviation>
<PDBx:bond_value>0.893</PDBx:bond_value>
<PDBx:label_alt_id_1></PDBx:label_alt_id_1>
<PDBx:label_alt_id_2></PDBx:label_alt_id_2>
<PDBx:linker_flag>N</PDBx:linker_flag>
</PDBx:pdbx_validate_rmsd_bond>
</PDBx:pdbx_validate_rmsd_bondCategory>
0
1
0
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
0
1
0
1
0
1
0
1
1
pdbx_validate_rmsd_bondCategory
This property indicates that datablock
has a category element pdbx_validate_rmsd_bond.
pdbx_validate_rmsd_bondItem
Abstract Datatype property for pdbx_validate_rmsd_bond items.
reference_to_pdbx_validate_rmsd_bond
cross-reference to pdbx_validate_rmsd_bond
pdbx_validate_rmsd_bond.PDB_ins_code_1
Optional identifier of the first of the two atom sites that
define the covalent bond.
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the
ATOM_SITE category.
pdbx_validate_rmsd_bond.PDB_ins_code_2
Optional identifier of the second of the two atom sites that
define the covalent bond.
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the
ATOM_SITE category.
pdbx_validate_rmsd_bond.PDB_model_num
The model number for the given bond
pdbx_validate_rmsd_bond.auth_asym_id_1
Part of the identifier of the first of the two atom sites that
define the covalent bond.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_rmsd_bond.auth_asym_id_2
Part of the identifier of the second of the two atom sites
that define the covalent bond.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_rmsd_bond.auth_atom_id_1
Part of the identifier of the first of the two atom sites that
define the covalent bond.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_rmsd_bond.auth_atom_id_2
Part of the identifier of the second of the two atom sites
that define the covalent bond.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_rmsd_bond.auth_comp_id_1
Part of the identifier of the first of the two atom sites that
define the covalent bond.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_rmsd_bond.auth_comp_id_2
Part of the identifier of the second of the two atom sites
that define the covalent bond.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_rmsd_bond.auth_seq_id_1
Part of the identifier of the first of the two atom sites that
define the covalent bond.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_rmsd_bond.auth_seq_id_2
Part of the identifier of the second of the two atom sites
that define the covalent bond.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_rmsd_bond.bond_deviation
The value of the deviation from ideal for the defined covalent
bond for the two atoms defined.
pdbx_validate_rmsd_bond.bond_value
The value of the bond length
pdbx_validate_rmsd_bond.label_alt_id_1
An optional identifier of the first of the two atoms that
define the covalent bond.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_rmsd_bond.label_alt_id_2
An optional identifier of the second of the two atoms that
define the covalent bond.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_rmsd_bond.linker_flag
A flag to indicate if the bond is between two residues
pdbx_validate_rmsd_bond.id
The value of attribute id in category pdbx_validate_rmsd_bond must uniquely identify
each item in the PDBX_VALIDATE_RMSD_BOND list.
This is an integer serial number.
pdbx_validate_symm_contact
Data items in the PDBX_VALIDATE_SYMM_CONTACT category list the
atoms within the entry that are in close contact with regard
the distances expected from either covalent bonding or closest
approach by van der Waals contacts. Contacts with
for symmetry related contacts are considered.
For those contacts not involving hydrogen a limit of
2.2 Angstroms is used. For contacts involving a hydrogen atom
a cutoff of 1.6Angstrom is used.
Example 1
<PDBx:pdbx_validate_symm_contactCategory>
<PDBx:pdbx_validate_symm_contact id="1">
<PDBx:PDB_ins_code_1></PDBx:PDB_ins_code_1>
<PDBx:PDB_ins_code_2></PDBx:PDB_ins_code_2>
<PDBx:PDB_model_num>1</PDBx:PDB_model_num>
<PDBx:auth_asym_id_1></PDBx:auth_asym_id_1>
<PDBx:auth_asym_id_2></PDBx:auth_asym_id_2>
<PDBx:auth_atom_id_1>O</PDBx:auth_atom_id_1>
<PDBx:auth_atom_id_2>O</PDBx:auth_atom_id_2>
<PDBx:auth_comp_id_1>HOH</PDBx:auth_comp_id_1>
<PDBx:auth_comp_id_2>HOH</PDBx:auth_comp_id_2>
<PDBx:auth_seq_id_1>70</PDBx:auth_seq_id_1>
<PDBx:auth_seq_id_2>70</PDBx:auth_seq_id_2>
<PDBx:dist>2.05</PDBx:dist>
<PDBx:label_alt_id_1></PDBx:label_alt_id_1>
<PDBx:label_alt_id_2></PDBx:label_alt_id_2>
<PDBx:site_symmetry_1>1555</PDBx:site_symmetry_1>
<PDBx:site_symmetry_2>7555</PDBx:site_symmetry_2>
</PDBx:pdbx_validate_symm_contact>
</PDBx:pdbx_validate_symm_contactCategory>
0
1
0
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
0
1
0
1
1
1
1
1
1
pdbx_validate_symm_contactCategory
This property indicates that datablock
has a category element pdbx_validate_symm_contact.
pdbx_validate_symm_contactItem
Abstract Datatype property for pdbx_validate_symm_contact items.
reference_to_pdbx_validate_symm_contact
cross-reference to pdbx_validate_symm_contact
pdbx_validate_symm_contact.PDB_ins_code_1
Optional identifier of the first of the two atom sites that
define the close contact.
pdbx_validate_symm_contact.PDB_ins_code_2
Optional identifier of the second of the two atom sites that
define the close contact.
pdbx_validate_symm_contact.PDB_model_num
The model number for the given angle
pdbx_validate_symm_contact.auth_asym_id_1
Part of the identifier of the first of the two atom sites that
define the close contact.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_symm_contact.auth_asym_id_2
Part of the identifier of the second of the two atom sites
that define the close contact.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_symm_contact.auth_atom_id_1
Part of the identifier of the first of the two atom sites that
define the close contact.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_symm_contact.auth_atom_id_2
Part of the identifier of the second of the two atom sites
that define the close contact.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_symm_contact.auth_comp_id_1
Part of the identifier of the first of the two atom sites that
define the close contact.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_symm_contact.auth_comp_id_2
Part of the identifier of the second of the two atom sites
that define the close contact.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_symm_contact.auth_seq_id_1
Part of the identifier of the first of the two atom sites that
define the close contact.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_symm_contact.auth_seq_id_2
Part of the identifier of the second of the two atom sites
that define the close contact.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_symm_contact.dist
The value of the close contact for the two atoms defined.
pdbx_validate_symm_contact.label_alt_id_1
An optional identifier of the first of the two atoms that
define the close contact.
This data item is a pointer to attribute label_alt.id in category atom_site in the
ATOM_SITE category.
pdbx_validate_symm_contact.label_alt_id_2
An optional identifier of the second of the two atoms that
define the close contact.
This data item is a pointer to attribute label_alt_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_symm_contact.site_symmetry_1
The symmetry of the first of the two atoms define the close contact.
Symmetry defined in ORTEP style of 555 equal to unit cell with translations
+-1 from 555 as 000
pdbx_validate_symm_contact.site_symmetry_2
The symmetry of the second of the two atoms define the close contact.
Symmetry defined in ORTEP style of 555 equal to unit cell with translations
+-1 from 555 as 000
pdbx_validate_symm_contact.id
The value of attribute id in category pdbx_validate_symm_contact must uniquely identify
each item in the PDBX_VALIDATE_SYMM_CONTACT list.
This is an integer serial number.
pdbx_validate_torsion
Data items in the PDBX_VALIDATE_TORSION category list the
residues with torsion angles outside the expected ramachandran regions
Example 1
<PDBx:pdbx_validate_torsionCategory>
<PDBx:pdbx_validate_torsion id="1">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:PDB_model_num>1</PDBx:PDB_model_num>
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_comp_id>SER</PDBx:auth_comp_id>
<PDBx:auth_seq_id>12</PDBx:auth_seq_id>
<PDBx:phi>-64.75</PDBx:phi>
<PDBx:psi>2.02</PDBx:psi>
</PDBx:pdbx_validate_torsion>
<PDBx:pdbx_validate_torsion id="2">
<PDBx:PDB_ins_code></PDBx:PDB_ins_code>
<PDBx:PDB_model_num>1</PDBx:PDB_model_num>
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_comp_id>THR</PDBx:auth_comp_id>
<PDBx:auth_seq_id>22</PDBx:auth_seq_id>
<PDBx:phi>-116.30</PDBx:phi>
<PDBx:psi>61.44</PDBx:psi>
</PDBx:pdbx_validate_torsion>
</PDBx:pdbx_validate_torsionCategory>
0
1
1
1
1
1
1
1
1
1
1
1
1
1
1
pdbx_validate_torsionCategory
This property indicates that datablock
has a category element pdbx_validate_torsion.
pdbx_validate_torsionItem
Abstract Datatype property for pdbx_validate_torsion items.
reference_to_pdbx_validate_torsion
cross-reference to pdbx_validate_torsion
pdbx_validate_torsion.PDB_ins_code
Optional identifier of the residue
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the
ATOM_SITE category.
pdbx_validate_torsion.PDB_model_num
The model number for the given residue
This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the
ATOM_SITE category.
pdbx_validate_torsion.auth_asym_id
Part of the identifier of the residue
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_torsion.auth_comp_id
Part of the identifier of the residue
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_torsion.auth_seq_id
Part of the identifier of the residue
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
pdbx_validate_torsion.phi
The Phi value that for the residue that lies outside normal limits
(in combination with the Psi value) with regards to the rammachandran plot
pdbx_validate_torsion.psi
The Psi value that for the residue that lies outside normal limits
(in combination with the Phi value) with regards to the rammachandran plot
pdbx_validate_torsion.id
The value of attribute id in category pdbx_validate_torsion must
uniquely identify each item in the PDBX_VALIDATE_TORSION list.
This is an integer serial number.
pdbx_version
Data items in the PDBX_VERSION category record details about the
current internal version of this entry.
Example 1 -
<PDBx:pdbx_versionCategory>
<PDBx:pdbx_version entry_id="1ABC" major_version="3" minor_version="12">
<PDBx:details> Update version information. </PDBx:details>
<PDBx:revision_date>2006-12-08</PDBx:revision_date>
</PDBx:pdbx_version>
</PDBx:pdbx_versionCategory>
0
1
1
1
1
1
1
pdbx_versionCategory
This property indicates that datablock
has a category element pdbx_version.
pdbx_versionItem
Abstract Datatype property for pdbx_version items.
reference_to_pdbx_version
cross-reference to pdbx_version
pdbx_version.details
A text description of any special details of the current version.
Includes new 3dem experimental data items
pdbx_version.revision_date
A date for the current version or revision. The date format is
yyyy-mm-dd.
2006-07-12
pdbx_version.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
pdbx_version.major_version
Major version number for this datablock:
3 - represents remediated data -
2 - current production data -
3
pdbx_version.minor_version
Minor version number for this datablock:
An integer value which is incremented for each
datablock revision.
15
pdbx_xplor_file
Parameter and topology files used in X-PLOR/CNS refinement.
<PDBx:pdbx_xplor_fileCategory>
<PDBx:pdbx_xplor_file pdbx_refine_id="x-ray" serial_no="1">
<PDBx:param_file>parm_hol.dat</PDBx:param_file>
<PDBx:topol_file>topol_hol.dat</PDBx:topol_file>
</PDBx:pdbx_xplor_file>
</PDBx:pdbx_xplor_fileCategory>
0
1
0
1
1
1
pdbx_xplor_fileCategory
This property indicates that datablock
has a category element pdbx_xplor_file.
pdbx_xplor_fileItem
Abstract Datatype property for pdbx_xplor_file items.
reference_to_pdbx_xplor_file
cross-reference to pdbx_xplor_file
pdbx_xplor_file.param_file
Parameter file name in X-PLOR/CNS refinement.
PARAM_NDBX_HIGH.DNA
pdbx_xplor_file.topol_file
Topology file name in X-PLOR/CNS refinement.
TOP_NDBX.DNA
pdbx_xplor_file.pdbx_refine_id
This data item uniquely identifies a refinement within an entry.
attribute pdbx_refine_id in category pdbx_xplor_file can be used to distinguish the results
of joint refinements.
pdbx_xplor_file.serial_no
Serial number.
phasing
Data items in the PHASING category record details about the
phasing of the structure, listing the various methods used in
the phasing process. Details about the application of each
method are listed in the appropriate subcategories.
Example 1 - hypothetical example.
<PDBx:phasingCategory>
<PDBx:phasing method="mir"></PDBx:phasing>
<PDBx:phasing method="averaging"></PDBx:phasing>
</PDBx:phasingCategory>
1
phasingCategory
This property indicates that datablock
has a category element phasing.
phasingItem
Abstract Datatype property for phasing items.
reference_to_phasing
cross-reference to phasing
phasing.method
A listing of the method or methods used to phase this
structure.
phasing by ab initio methods
abinitio
phase improvement by averaging over multiple
images of the structure
averaging
phasing by direct methods
dm
phasing by iterative single-wavelength
anomalous scattering
isas
phasing by iterative single-wavelength
isomorphous replacement
isir
phasing beginning with phases calculated from
an isomorphous structure
isomorphous
phasing by multiple-wavelength anomalous
dispersion
mad
phasing by multiple isomorphous replacement
mir
phasing by multiple isomorphous replacement
with anomalous scattering
miras
phasing by molecular replacement
mr
phasing by single isomorphous replacement
sir
phasing by single isomorphous replacement
with anomalous scattering
siras
phasing_MAD
Data items in the PHASING_MAD category record details about
the phasing of the structure where methods involving
multiple-wavelength anomalous-dispersion techniques are involved.
Example 1 - based on a paper by Shapiro et al. [Nature (London)
(1995), 374, 327-337].
<PDBx:phasing_MADCategory>
<PDBx:phasing_MAD entry_id="NCAD"></PDBx:phasing_MAD>
</PDBx:phasing_MADCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
phasing_MADCategory
This property indicates that datablock
has a category element phasing_MAD.
phasing_MADItem
Abstract Datatype property for phasing_MAD items.
reference_to_phasing_MAD
cross-reference to phasing_MAD
phasing_MAD.details
A description of special aspects of the MAD phasing.
phasing_MAD.method
A description of the MAD phasing method used to phase
this structure.
Note that this is not the computer program used, which is
described in the SOFTWARE category, but rather the method
itself.
This data item should be used to describe significant
methodological options used within the MAD phasing program.
phasing_MAD.pdbx_R_cullis
attribute pdbx_R_cullis in category phasing_MAD records R_cullis
for MAD phasing.
phasing_MAD.pdbx_R_cullis_acentric
attribute pdbx_R_cullis_acentric in category phasing_MAD records R_cullis
using acentric data for MAD phasing.
phasing_MAD.pdbx_R_cullis_centric
attribute pdbx_R_cullis_centric in category phasing_MAD records R_cullis
using centric data for MAD phasing.
phasing_MAD.pdbx_R_kraut
attribute pdbx_R_kraut in category phasing_MAD records R_kraut
for MAD phasing.
phasing_MAD.pdbx_R_kraut_acentric
attribute pdbx_R_kraut_acentric in category phasing_MAD records R_kraut
using acentric data for MAD phasing.
phasing_MAD.pdbx_R_kraut_centric
attribute pdbx_R_kraut_centric in category phasing_MAD records R_kraut
using centric data for MAD phasing.
phasing_MAD.pdbx_anom_scat_method
attribute pdbx_anom_scat_method in category phasing_MAD records the method
used to locate anomalous scatterers for MAD phasing.
phasing_MAD.pdbx_d_res_high
attribute pdbx_d_res_high in category phasing_MAD records the highest resolution
for MAD phasing.
phasing_MAD.pdbx_d_res_low
attribute pdbx_d_res_low in category phasing_MAD records the lowest resolution
for MAD phasing.
phasing_MAD.pdbx_fom
attribute pdbx_fom in category phasing_MAD records the figure of merit
for MAD phasing.
phasing_MAD.pdbx_fom_acentric
attribute pdbx_fom_acentric in category phasing_MAD records the figure of merit
using acentric data for MAD phasing.
phasing_MAD.pdbx_fom_centric
attribute pdbx_fom_centric in category phasing_MAD records the figure of merit
using centric data for MAD phasing.
phasing_MAD.pdbx_loc
attribute pdbx_loc in category phasing_MAD records lack of closure
for MAD phasing.
phasing_MAD.pdbx_loc_acentric
attribute pdbx_loc_acentric in category phasing_MAD records lack of closure
using acentric data for MAD phasing.
phasing_MAD.pdbx_loc_centric
attribute pdbx_loc_centric in category phasing_MAD records lack of closure
using centric data for MAD phasing.
phasing_MAD.pdbx_number_data_sets
attribute pdbx_loc in category phasing_MAD records the number
of data sets used for MAD phasing.
phasing_MAD.pdbx_power
attribute pdbx_power in category phasing_MAD records phasing power
for MAD phasing.
phasing_MAD.pdbx_power_acentric
attribute pdbx_power_acentric in category phasing_MAD records phasing power
using acentric data for MAD phasing.
phasing_MAD.pdbx_power_centric
attribute pdbx_power_centric in category phasing_MAD records phasing power
using centric data for MAD phasing.
phasing_MAD.pdbx_reflns
attribute pdbx_reflns in category phasing_MAD records the number of
reflections used for MAD phasing.
phasing_MAD.pdbx_reflns_acentric
attribute pdbx_reflns_acentric in category phasing_MAD records the number of
acentric reflections for MAD phasing.
phasing_MAD.pdbx_reflns_centric
attribute pdbx_reflns_centric in category phasing_MAD records the number of
centric reflections for MAD phasing.
phasing_MAD.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
phasing_MAD_clust
Data items in the PHASING_MAD_CLUST category record details
about a cluster of experiments that contributed to the
generation of a set of phases.
Example 1 - based on a paper by Shapiro et al. [Nature (London)
(1995), 374, 327-337].
<PDBx:phasing_MAD_clustCategory>
<PDBx:phasing_MAD_clust expt_id="1" id="4 wavelength">
<PDBx:number_set>4</PDBx:number_set>
</PDBx:phasing_MAD_clust>
<PDBx:phasing_MAD_clust expt_id="1" id="5 wavelength">
<PDBx:number_set>5</PDBx:number_set>
</PDBx:phasing_MAD_clust>
<PDBx:phasing_MAD_clust expt_id="2" id="5 wavelength">
<PDBx:number_set>5</PDBx:number_set>
</PDBx:phasing_MAD_clust>
</PDBx:phasing_MAD_clustCategory>
0
1
1
1
phasing_MAD_clustCategory
This property indicates that datablock
has a category element phasing_MAD_clust.
phasing_MAD_clustItem
Abstract Datatype property for phasing_MAD_clust items.
reference_to_phasing_MAD_clust
cross-reference to phasing_MAD_clust
phasing_MAD_clust.number_set
The number of data sets in this cluster of data sets.
phasing_MAD_clust.expt_id
This data item is a pointer to attribute id in category phasing_MAD_expt in the
PHASING_MAD_EXPT category.
phasing_MAD_clust.id
The value of attribute id in category phasing_MAD_clust must, together with
attribute expt_id in category phasing_MAD_clust, uniquely identify a record in the
PHASING_MAD_CLUST list.
Note that this item need not be a number; it can be any unique
identifier.
phasing_MAD_expt
Data items in the PHASING_MAD_EXPT category record details about
a MAD phasing experiment, such as the number of experiments that
were clustered together to produce a set of phases or the
statistics for those phases.
Example 1 - based on a paper by Shapiro et al. [Nature (London)
(1995), 374, 327-337].
<PDBx:phasing_MAD_exptCategory>
<PDBx:phasing_MAD_expt id="1">
<PDBx:R_normal_all>0.063</PDBx:R_normal_all>
<PDBx:R_normal_anom_scat>0.451</PDBx:R_normal_anom_scat>
<PDBx:delta_delta_phi>58.5</PDBx:delta_delta_phi>
<PDBx:delta_phi_sigma>20.3</PDBx:delta_phi_sigma>
<PDBx:mean_fom>0.88</PDBx:mean_fom>
<PDBx:number_clust>2</PDBx:number_clust>
</PDBx:phasing_MAD_expt>
<PDBx:phasing_MAD_expt id="2">
<PDBx:R_normal_all>0.051</PDBx:R_normal_all>
<PDBx:R_normal_anom_scat>0.419</PDBx:R_normal_anom_scat>
<PDBx:delta_delta_phi>36.8</PDBx:delta_delta_phi>
<PDBx:delta_phi_sigma>18.2</PDBx:delta_phi_sigma>
<PDBx:mean_fom>0.93</PDBx:mean_fom>
<PDBx:number_clust>1</PDBx:number_clust>
</PDBx:phasing_MAD_expt>
</PDBx:phasing_MAD_exptCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
phasing_MAD_exptCategory
This property indicates that datablock
has a category element phasing_MAD_expt.
phasing_MAD_exptItem
Abstract Datatype property for phasing_MAD_expt items.
reference_to_phasing_MAD_expt
cross-reference to phasing_MAD_expt
phasing_MAD_expt.R_normal_all
Definition...
phasing_MAD_expt.R_normal_anom_scat
Definition...
phasing_MAD_expt.delta_delta_phi
The difference between two independent determinations of
attribute delta_phi in category phasing_MAD_expt.
phasing_MAD_expt.delta_phi
The phase difference between F~t~(h), the structure factor due
to normal scattering from all atoms, and F~a~(h), the structure
factor due to normal scattering from only the anomalous
scatterers.
phasing_MAD_expt.delta_phi_sigma
The standard uncertainty (estimated standard deviation)
of attribute delta_phi in category phasing_MAD_expt.
phasing_MAD_expt.mean_fom
The mean figure of merit.
phasing_MAD_expt.number_clust
The number of clusters of data sets in this phasing experiment.
phasing_MAD_expt.id
The value of attribute id in category phasing_MAD_expt must uniquely identify each
record in the PHASING_MAD_EXPT list.
phasing_MAD_ratio
Data items in the PHASING_MAD_RATIO category record
the ratios of phasing statistics between pairs of data sets
in a MAD phasing experiment, in given shells of resolution.
Example 1 - based on a paper by Shapiro et al. [Nature (London)
(1995), 374, 327-337].
<PDBx:phasing_MAD_ratioCategory>
<PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.4013" wavelength_2="1.4013">
<PDBx:d_res_high>4.00</PDBx:d_res_high>
<PDBx:d_res_low>20.00</PDBx:d_res_low>
<PDBx:ratio_one_wl>0.084</PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric>0.076</PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl></PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.4013" wavelength_2="1.3857">
<PDBx:d_res_high>4.00</PDBx:d_res_high>
<PDBx:d_res_low>20.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.067</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.4013" wavelength_2="1.3852">
<PDBx:d_res_high>4.00</PDBx:d_res_high>
<PDBx:d_res_low>20.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.051</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.4013" wavelength_2="1.3847">
<PDBx:d_res_high>4.00</PDBx:d_res_high>
<PDBx:d_res_low>20.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.044</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3857">
<PDBx:d_res_high>4.00</PDBx:d_res_high>
<PDBx:d_res_low>20.00</PDBx:d_res_low>
<PDBx:ratio_one_wl>0.110</PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric>0.049</PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl></PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3852">
<PDBx:d_res_high>4.00</PDBx:d_res_high>
<PDBx:d_res_low>20.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.049</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3847">
<PDBx:d_res_high>4.00</PDBx:d_res_high>
<PDBx:d_res_low>20.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.067</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3852">
<PDBx:d_res_high>4.00</PDBx:d_res_high>
<PDBx:d_res_low>20.00</PDBx:d_res_low>
<PDBx:ratio_one_wl>0.149</PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric>0.072</PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl></PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3847">
<PDBx:d_res_high>4.00</PDBx:d_res_high>
<PDBx:d_res_low>20.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.039</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3847" wavelength_2="1.3847">
<PDBx:d_res_high>4.00</PDBx:d_res_high>
<PDBx:d_res_low>20.00</PDBx:d_res_low>
<PDBx:ratio_one_wl>0.102</PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric>0.071</PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl></PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.4013" wavelength_2="1.4013">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>4.00</PDBx:d_res_low>
<PDBx:ratio_one_wl>0.114</PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric>0.111</PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl></PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.4013" wavelength_2="1.3857">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>4.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.089</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.4013" wavelength_2="1.3852">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>4.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.086</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.4013" wavelength_2="1.3847">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>4.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.077</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3857">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>4.00</PDBx:d_res_low>
<PDBx:ratio_one_wl>0.140</PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric>0.127</PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl></PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3852">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>4.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.085</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3847">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>4.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.089</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3852">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>4.00</PDBx:d_res_low>
<PDBx:ratio_one_wl>0.155</PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric>0.119</PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl></PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3847">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>4.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.082</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3847" wavelength_2="1.3847">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>4.00</PDBx:d_res_low>
<PDBx:ratio_one_wl>0.124</PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric>0.120</PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl></PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3857">
<PDBx:d_res_high>4.00</PDBx:d_res_high>
<PDBx:d_res_low>20.00</PDBx:d_res_low>
<PDBx:ratio_one_wl>0.075</PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric>0.027</PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl></PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3852">
<PDBx:d_res_high>4.00</PDBx:d_res_high>
<PDBx:d_res_low>20.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.041</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3847">
<PDBx:d_res_high>4.00</PDBx:d_res_high>
<PDBx:d_res_low>20.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.060</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3784">
<PDBx:d_res_high>4.00</PDBx:d_res_high>
<PDBx:d_res_low>20.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.057</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.2862">
<PDBx:d_res_high>4.00</PDBx:d_res_high>
<PDBx:d_res_low>20.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.072</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3852">
<PDBx:d_res_high>4.00</PDBx:d_res_high>
<PDBx:d_res_low>20.00</PDBx:d_res_low>
<PDBx:ratio_one_wl>0.105</PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric>0.032</PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl></PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3847">
<PDBx:d_res_high>4.00</PDBx:d_res_high>
<PDBx:d_res_low>20.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.036</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3784">
<PDBx:d_res_high>4.00</PDBx:d_res_high>
<PDBx:d_res_low>20.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.044</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.2862">
<PDBx:d_res_high>4.00</PDBx:d_res_high>
<PDBx:d_res_low>20.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.065</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3847" wavelength_2="1.3847">
<PDBx:d_res_high>4.00</PDBx:d_res_high>
<PDBx:d_res_low>20.00</PDBx:d_res_low>
<PDBx:ratio_one_wl>0.072</PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric>0.031</PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl></PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3847" wavelength_2="1.3784">
<PDBx:d_res_high>4.00</PDBx:d_res_high>
<PDBx:d_res_low>20.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.040</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3847" wavelength_2="1.2862">
<PDBx:d_res_high>4.00</PDBx:d_res_high>
<PDBx:d_res_low>20.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.059</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3784" wavelength_2="1.3784">
<PDBx:d_res_high>4.00</PDBx:d_res_high>
<PDBx:d_res_low>20.00</PDBx:d_res_low>
<PDBx:ratio_one_wl>0.059</PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric>0.032</PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl></PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3784" wavelength_2="1.2862">
<PDBx:d_res_high>4.00</PDBx:d_res_high>
<PDBx:d_res_low>20.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.059</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.2862" wavelength_2="1.3847">
<PDBx:d_res_high>4.00</PDBx:d_res_high>
<PDBx:d_res_low>20.00</PDBx:d_res_low>
<PDBx:ratio_one_wl>0.058</PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric>0.028</PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl></PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3857">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>4.00</PDBx:d_res_low>
<PDBx:ratio_one_wl>0.078</PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric>0.075</PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl></PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3852">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>4.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.059</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3847">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>4.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.067</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3784">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>4.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.084</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.2862">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>4.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.073</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3852">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>4.00</PDBx:d_res_low>
<PDBx:ratio_one_wl>0.101</PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric>0.088</PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl></PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3847">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>4.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.066</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3784">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>4.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.082</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.2862">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>4.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.085</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3847" wavelength_2="1.3847">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>4.00</PDBx:d_res_low>
<PDBx:ratio_one_wl>0.097</PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric>0.074</PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl></PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3847" wavelength_2="1.3784">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>4.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.081</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3847" wavelength_2="1.2862">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>4.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.085</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3784" wavelength_2="1.3784">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>4.00</PDBx:d_res_low>
<PDBx:ratio_one_wl>0.114</PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric>0.089</PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl></PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3784" wavelength_2="1.2862">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>4.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.103</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.2862" wavelength_2="1.2862">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>4.00</PDBx:d_res_low>
<PDBx:ratio_one_wl>0.062</PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric>0.060</PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl></PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7263">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>15.00</PDBx:d_res_low>
<PDBx:ratio_one_wl>0.035</PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric>0.026</PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl></PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7251">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>15.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.028</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7284">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>15.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.023</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7246">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>15.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.025</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7217">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>15.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.026</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7251" wavelength_2="0.7251">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>15.00</PDBx:d_res_low>
<PDBx:ratio_one_wl>0.060</PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric>0.026</PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl></PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7251" wavelength_2="0.7284">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>15.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.029</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7251" wavelength_2="0.7246">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>15.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.031</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7251" wavelength_2="0.7217">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>15.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.035</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7284" wavelength_2="0.7284">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>15.00</PDBx:d_res_low>
<PDBx:ratio_one_wl>0.075</PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric>0.030</PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl></PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7284" wavelength_2="0.7246">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>15.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.023</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7284" wavelength_2="0.7217">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>15.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.027</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7246" wavelength_2="0.7246">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>15.00</PDBx:d_res_low>
<PDBx:ratio_one_wl>0.069</PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric>0.026</PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl></PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7246" wavelength_2="0.7217">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>15.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.024</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7217" wavelength_2="0.7284">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>15.00</PDBx:d_res_low>
<PDBx:ratio_one_wl>0.060</PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric>0.028</PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl></PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7263">
<PDBx:d_res_high>1.90</PDBx:d_res_high>
<PDBx:d_res_low>3.00</PDBx:d_res_low>
<PDBx:ratio_one_wl>0.060</PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric>0.050</PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl></PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7251">
<PDBx:d_res_high>1.90</PDBx:d_res_high>
<PDBx:d_res_low>3.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.056</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7284">
<PDBx:d_res_high>1.90</PDBx:d_res_high>
<PDBx:d_res_low>3.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.055</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7246">
<PDBx:d_res_high>1.90</PDBx:d_res_high>
<PDBx:d_res_low>3.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.053</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7217">
<PDBx:d_res_high>1.90</PDBx:d_res_high>
<PDBx:d_res_low>3.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.056</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7251" wavelength_2="0.7251">
<PDBx:d_res_high>1.90</PDBx:d_res_high>
<PDBx:d_res_low>3.00</PDBx:d_res_low>
<PDBx:ratio_one_wl>0.089</PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric>0.050</PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl></PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7251" wavelength_2="0.7284">
<PDBx:d_res_high>1.90</PDBx:d_res_high>
<PDBx:d_res_low>3.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.054</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7251" wavelength_2="0.7246">
<PDBx:d_res_high>1.90</PDBx:d_res_high>
<PDBx:d_res_low>3.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.058</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7251" wavelength_2="0.7217">
<PDBx:d_res_high>1.90</PDBx:d_res_high>
<PDBx:d_res_low>3.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.063</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7284" wavelength_2="0.7284">
<PDBx:d_res_high>1.90</PDBx:d_res_high>
<PDBx:d_res_low>3.00</PDBx:d_res_low>
<PDBx:ratio_one_wl>0.104</PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric>0.057</PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl></PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7284" wavelength_2="0.7246">
<PDBx:d_res_high>1.90</PDBx:d_res_high>
<PDBx:d_res_low>3.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.052</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7284" wavelength_2="0.7217">
<PDBx:d_res_high>1.90</PDBx:d_res_high>
<PDBx:d_res_low>3.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.057</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7246" wavelength_2="0.7246">
<PDBx:d_res_high>1.90</PDBx:d_res_high>
<PDBx:d_res_low>3.00</PDBx:d_res_low>
<PDBx:ratio_one_wl>0.098</PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric>0.052</PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl></PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7246" wavelength_2="0.7217">
<PDBx:d_res_high>1.90</PDBx:d_res_high>
<PDBx:d_res_low>3.00</PDBx:d_res_low>
<PDBx:ratio_one_wl></PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric></PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl>0.054</PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
<PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7217" wavelength_2="0.7284">
<PDBx:d_res_high>1.90</PDBx:d_res_high>
<PDBx:d_res_low>3.00</PDBx:d_res_low>
<PDBx:ratio_one_wl>0.089</PDBx:ratio_one_wl>
<PDBx:ratio_one_wl_centric>0.060</PDBx:ratio_one_wl_centric>
<PDBx:ratio_two_wl></PDBx:ratio_two_wl>
</PDBx:phasing_MAD_ratio>
</PDBx:phasing_MAD_ratioCategory>
0
1
0
1
0
1
0
1
0
1
1
1
1
1
phasing_MAD_ratioCategory
This property indicates that datablock
has a category element phasing_MAD_ratio.
phasing_MAD_ratioItem
Abstract Datatype property for phasing_MAD_ratio items.
reference_to_phasing_MAD_ratio
cross-reference to phasing_MAD_ratio
phasing_MAD_ratio.d_res_high
The lowest value for the interplanar spacings for the
reflection data used for the comparison of Bijvoet differences.
This is called the highest resolution.
phasing_MAD_ratio.d_res_low
The highest value for the interplanar spacings for the
reflection data used for the comparison of Bijvoet differences.
This is called the lowest resolution.
phasing_MAD_ratio.ratio_one_wl
The root-mean-square Bijvoet difference at one wavelength for
all reflections.
phasing_MAD_ratio.ratio_one_wl_centric
The root-mean-square Bijvoet difference at one wavelength for
centric reflections. This would be equal to zero for perfect
data and thus serves as an estimate of the noise in the
anomalous signals.
phasing_MAD_ratio.ratio_two_wl
The root-mean-square dispersive Bijvoet difference between
two wavelengths for all reflections.
phasing_MAD_ratio.clust_id
This data item is a pointer to attribute id in category phasing_MAD_clust in
the PHASING_MAD_CLUST category.
phasing_MAD_ratio.expt_id
This data item is a pointer to attribute id in category phasing_MAD_expt in the
PHASING_MAD_EXPT category.
phasing_MAD_ratio.wavelength_1
This data item is a pointer to attribute wavelength in category phasing_MAD_set in
the PHASING_MAD_SET category.
phasing_MAD_ratio.wavelength_2
This data item is a pointer to attribute wavelength in category phasing_MAD_set in
the PHASING_MAD_SET category.
phasing_MAD_set
Data items in the PHASING_MAD_SET category record
details about the individual data sets used in a MAD phasing
experiment.
Example 1 - based on a paper by Shapiro et al. [Nature (London)
(1995), 374, 327-337].
<PDBx:phasing_MAD_setCategory>
<PDBx:phasing_MAD_set clust_id="4 wavelength" expt_id="1" set_id="aa" wavelength="1.4013">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>20.00</PDBx:d_res_low>
<PDBx:f_double_prime>3.80</PDBx:f_double_prime>
<PDBx:f_prime>-12.48</PDBx:f_prime>
<PDBx:wavelength_details>pre-edge</PDBx:wavelength_details>
</PDBx:phasing_MAD_set>
<PDBx:phasing_MAD_set clust_id="4 wavelength" expt_id="1" set_id="bb" wavelength="1.3857">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>20.00</PDBx:d_res_low>
<PDBx:f_double_prime>17.20</PDBx:f_double_prime>
<PDBx:f_prime>-31.22</PDBx:f_prime>
<PDBx:wavelength_details>peak</PDBx:wavelength_details>
</PDBx:phasing_MAD_set>
<PDBx:phasing_MAD_set clust_id="4 wavelength" expt_id="1" set_id="cc" wavelength="1.3852">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>20.00</PDBx:d_res_low>
<PDBx:f_double_prime>29.17</PDBx:f_double_prime>
<PDBx:f_prime>-13.97</PDBx:f_prime>
<PDBx:wavelength_details>edge</PDBx:wavelength_details>
</PDBx:phasing_MAD_set>
<PDBx:phasing_MAD_set clust_id="4 wavelength" expt_id="1" set_id="dd" wavelength="1.3847">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>20.00</PDBx:d_res_low>
<PDBx:f_double_prime>17.34</PDBx:f_double_prime>
<PDBx:f_prime>-6.67</PDBx:f_prime>
<PDBx:wavelength_details>remote</PDBx:wavelength_details>
</PDBx:phasing_MAD_set>
<PDBx:phasing_MAD_set clust_id="5 wavelength" expt_id="1" set_id="ee" wavelength="1.3857">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>20.00</PDBx:d_res_low>
<PDBx:f_double_prime>14.84</PDBx:f_double_prime>
<PDBx:f_prime>-28.33</PDBx:f_prime>
<PDBx:wavelength_details>ascending edge</PDBx:wavelength_details>
</PDBx:phasing_MAD_set>
<PDBx:phasing_MAD_set clust_id="5 wavelength" expt_id="1" set_id="ff" wavelength="1.3852">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>20.00</PDBx:d_res_low>
<PDBx:f_double_prime>30.23</PDBx:f_double_prime>
<PDBx:f_prime>-21.50</PDBx:f_prime>
<PDBx:wavelength_details>peak</PDBx:wavelength_details>
</PDBx:phasing_MAD_set>
<PDBx:phasing_MAD_set clust_id="5 wavelength" expt_id="1" set_id="gg" wavelength="1.3847">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>20.00</PDBx:d_res_low>
<PDBx:f_double_prime>20.35</PDBx:f_double_prime>
<PDBx:f_prime>-10.71</PDBx:f_prime>
<PDBx:wavelength_details>descending edge</PDBx:wavelength_details>
</PDBx:phasing_MAD_set>
<PDBx:phasing_MAD_set clust_id="5 wavelength" expt_id="1" set_id="hh" wavelength="1.3784">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>20.00</PDBx:d_res_low>
<PDBx:f_double_prime>11.84</PDBx:f_double_prime>
<PDBx:f_prime>-14.45</PDBx:f_prime>
<PDBx:wavelength_details>remote 1</PDBx:wavelength_details>
</PDBx:phasing_MAD_set>
<PDBx:phasing_MAD_set clust_id="5 wavelength" expt_id="1" set_id="ii" wavelength="1.2862">
<PDBx:d_res_high>3.00</PDBx:d_res_high>
<PDBx:d_res_low>20.00</PDBx:d_res_low>
<PDBx:f_double_prime>9.01</PDBx:f_double_prime>
<PDBx:f_prime>-9.03</PDBx:f_prime>
<PDBx:wavelength_details>remote 2</PDBx:wavelength_details>
</PDBx:phasing_MAD_set>
<PDBx:phasing_MAD_set clust_id="5 wavelength" expt_id="2" set_id="jj" wavelength="0.7263">
<PDBx:d_res_high>1.90</PDBx:d_res_high>
<PDBx:d_res_low>15.00</PDBx:d_res_low>
<PDBx:f_double_prime>4.08</PDBx:f_double_prime>
<PDBx:f_prime>-21.10</PDBx:f_prime>
<PDBx:wavelength_details>pre-edge</PDBx:wavelength_details>
</PDBx:phasing_MAD_set>
<PDBx:phasing_MAD_set clust_id="5 wavelength" expt_id="2" set_id="kk" wavelength="0.7251">
<PDBx:d_res_high>1.90</PDBx:d_res_high>
<PDBx:d_res_low>15.00</PDBx:d_res_low>
<PDBx:f_double_prime>7.92</PDBx:f_double_prime>
<PDBx:f_prime>-34.72</PDBx:f_prime>
<PDBx:wavelength_details>edge</PDBx:wavelength_details>
</PDBx:phasing_MAD_set>
<PDBx:phasing_MAD_set clust_id="5 wavelength" expt_id="2" set_id="ll" wavelength="0.7248">
<PDBx:d_res_high>1.90</PDBx:d_res_high>
<PDBx:d_res_low>15.00</PDBx:d_res_low>
<PDBx:f_double_prime>10.30</PDBx:f_double_prime>
<PDBx:f_prime>-24.87</PDBx:f_prime>
<PDBx:wavelength_details>peak</PDBx:wavelength_details>
</PDBx:phasing_MAD_set>
<PDBx:phasing_MAD_set clust_id="5 wavelength" expt_id="2" set_id="mm" wavelength="0.7246">
<PDBx:d_res_high>1.90</PDBx:d_res_high>
<PDBx:d_res_low>15.00</PDBx:d_res_low>
<PDBx:f_double_prime>9.62</PDBx:f_double_prime>
<PDBx:f_prime>-17.43</PDBx:f_prime>
<PDBx:wavelength_details>descending edge</PDBx:wavelength_details>
</PDBx:phasing_MAD_set>
<PDBx:phasing_MAD_set clust_id="5 wavelength" expt_id="2" set_id="nn" wavelength="0.7217">
<PDBx:d_res_high>1.90</PDBx:d_res_high>
<PDBx:d_res_low>15.00</PDBx:d_res_low>
<PDBx:f_double_prime>8.40</PDBx:f_double_prime>
<PDBx:f_prime>-13.26</PDBx:f_prime>
<PDBx:wavelength_details>remote</PDBx:wavelength_details>
</PDBx:phasing_MAD_set>
</PDBx:phasing_MAD_setCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
phasing_MAD_setCategory
This property indicates that datablock
has a category element phasing_MAD_set.
phasing_MAD_setItem
Abstract Datatype property for phasing_MAD_set items.
reference_to_phasing_MAD_set
cross-reference to phasing_MAD_set
phasing_MAD_set.d_res_high
The lowest value for the interplanar spacings for the
reflection data used for this set of data. This is called
the highest resolution.
phasing_MAD_set.d_res_low
The highest value for the interplanar spacings for the
reflection data used for this set of data. This is called
the lowest resolution.
phasing_MAD_set.f_double_prime
The f'' component of the anomalous scattering factor for this
wavelength.
phasing_MAD_set.f_prime
The f' component of the anomalous scattering factor for this
wavelength.
phasing_MAD_set.pdbx_atom_type
record the type of heavy atoms which produce anomolous singal.
phasing_MAD_set.pdbx_f_double_prime_refined
record the refined f_double_prime (not from experiment).
phasing_MAD_set.pdbx_f_prime_refined
record the refined f_prime (not from experiment).
phasing_MAD_set.wavelength_details
A descriptor for this wavelength in this cluster of data sets.
peak
remote
ascending edge
phasing_MAD_set.clust_id
This data item is a pointer to attribute id in category phasing_MAD_clust in
the PHASING_MAD_CLUST category.
phasing_MAD_set.expt_id
This data item is a pointer to attribute id in category phasing_MAD_expt in the
PHASING_MAD_EXPT category.
phasing_MAD_set.set_id
This data item is a pointer to attribute id in category phasing_set in the
PHASING_SET category.
phasing_MAD_set.wavelength
The wavelength at which this data set was measured.
phasing_MIR
Data items in the PHASING_MIR category record details about
the phasing of the structure where methods involving isomorphous
replacement are involved.
All isomorphous-replacement-based techniques are covered
by this category, including single isomorphous replacement (SIR),
multiple isomorphous replacement (MIR) and single or multiple
isomorphous replacement plus anomalous scattering (SIRAS, MIRAS).
Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem.
(1993), 268, 10728-10738].
<PDBx:phasing_MIRCategory>
<PDBx:phasing_MIR entry_id="1ABC">
<PDBx:method> Standard phase refinement (Blow & Crick, 1959)</PDBx:method>
</PDBx:phasing_MIR>
</PDBx:phasing_MIRCategory>
0
1
0
1
0
1
1
1
1
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
phasing_MIRCategory
This property indicates that datablock
has a category element phasing_MIR.
phasing_MIRItem
Abstract Datatype property for phasing_MIR items.
reference_to_phasing_MIR
cross-reference to phasing_MIR
phasing_MIR.FOM
The mean value of the figure of merit m for all reflections
phased in the native data set.
int P~alpha~ exp(i*alpha) dalpha
m = --------------------------------
int P~alpha~ dalpha
P~a~ = the probability that the phase angle a is correct
the integral is taken over the range alpha = 0 to 2 pi.
phasing_MIR.FOM_acentric
The mean value of the figure of merit m for the acentric
reflections phased in the native data set.
int P~alpha~ exp(i*alpha) dalpha
m = --------------------------------
int P~alpha~ dalpha
P~a~ = the probability that the phase angle a is correct
the integral is taken over the range alpha = 0 to 2 pi.
phasing_MIR.FOM_centric
The mean value of the figure of merit m for the centric
reflections phased in the native data set.
int P~alpha~ exp(i*alpha) dalpha
m = --------------------------------
int P~alpha~ dalpha
P~a~ = the probability that the phase angle a is correct
the integral is taken over the range alpha = 0 to 2 pi.
phasing_MIR.d_res_high
The lowest value in angstroms for the interplanar spacings
for the reflection data used for the native data set. This is
called the highest resolution.
phasing_MIR.d_res_low
The highest value in angstroms for the interplanar spacings
for the reflection data used for the native data set. This is
called the lowest resolution.
phasing_MIR.details
A description of special aspects of the isomorphous-replacement
phasing.
phasing_MIR.method
A description of the MIR phasing method applied to phase this
structure.
Note that this is not the computer program used, which is
described in the SOFTWARE category, but rather the method
itself.
This data item should be used to describe significant
methodological options used within the MIR phasing program.
phasing_MIR.pdbx_number_derivatives
The number of derivatives used in this phasing experiment.
phasing_MIR.reflns
The total number of reflections phased in the native data set.
phasing_MIR.reflns_acentric
The number of acentric reflections phased in the native data
set.
phasing_MIR.reflns_centric
The number of centric reflections phased in the native data
set.
phasing_MIR.reflns_criterion
Criterion used to limit the reflections used in the phasing
calculations.
> 4 \s(I)
phasing_MIR.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
phasing_MIR_der
Data items in the PHASING_MIR_DER category record details
about individual derivatives used in the phasing of the
structure when methods involving isomorphous replacement are
involved.
A derivative in this context does not necessarily equate with
a data set; for instance, the same data set could be used to
one resolution limit as an isomorphous scatterer and to a
different resolution (and with a different sigma cutoff) as an
anomalous scatterer. These would be treated as two distinct
derivatives, although both derivatives would point to the same
data sets via attribute der_set_id in category phasing_MIR_der and
attribute native_set_id in category phasing_MIR_der.
Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem.
(1993), 268, 10728-10738].
<PDBx:phasing_MIR_derCategory>
<PDBx:phasing_MIR_der id="KAu(CN)2">
<PDBx:details>major site interpreted in difference Patterson</PDBx:details>
<PDBx:number_of_sites>3</PDBx:number_of_sites>
</PDBx:phasing_MIR_der>
<PDBx:phasing_MIR_der id="K2HgI4">
<PDBx:details>sites found in cross-difference Fourier</PDBx:details>
<PDBx:number_of_sites>6</PDBx:number_of_sites>
</PDBx:phasing_MIR_der>
<PDBx:phasing_MIR_der id="K3IrCl6">
<PDBx:details>sites found in cross-difference Fourier</PDBx:details>
<PDBx:number_of_sites>2</PDBx:number_of_sites>
</PDBx:phasing_MIR_der>
<PDBx:phasing_MIR_der id="All">
<PDBx:details>data for all three derivatives combined</PDBx:details>
<PDBx:number_of_sites>11</PDBx:number_of_sites>
</PDBx:phasing_MIR_der>
</PDBx:phasing_MIR_derCategory>
0
1
0
1
0
1
1
1
1
1
1
1
0
1
1
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
phasing_MIR_derCategory
This property indicates that datablock
has a category element phasing_MIR_der.
phasing_MIR_derItem
Abstract Datatype property for phasing_MIR_der items.
reference_to_phasing_MIR_der
cross-reference to phasing_MIR_der
phasing_MIR_der.R_cullis_acentric
Residual factor R~cullis,acen~ for acentric reflections for this
derivative.
The Cullis R factor was originally defined only for centric
reflections. It is, however, also a useful statistical
measure for acentric reflections, which is how it is used in
this data item.
sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ |
R~cullis,acen~ = ----------------------------------------
sum|Fph~obs~ - Fp~obs~|
Fp~obs~ = the observed structure-factor amplitude of the native
Fph~obs~ = the observed structure-factor amplitude of the
derivative
Fh~calc~ = the calculated structure-factor amplitude from the
heavy-atom model
sum is taken over the specified reflections
Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G.
& North, A. C. T. (1961). Proc. R. Soc. London Ser. A,
265, 15-38.
phasing_MIR_der.R_cullis_anomalous
Residual factor R~cullis,ano~ for anomalous reflections for this
derivative.
The Cullis R factor was originally defined only for centric
reflections. It is, however, also a useful statistical
measure for anomalous reflections, which is how it is used in
this data item.
This is tabulated for acentric terms. A value less than 1.0
means there is some contribution to the phasing from the
anomalous data.
sum |Fph+~obs~Fph-~obs~ - Fh+~calc~ - Fh-~calc~|
R~cullis,ano~ = ------------------------------------------------
sum|Fph+~obs~ - Fph-~obs~|
Fph+~obs~ = the observed positive Friedel structure-factor
amplitude for the derivative
Fph-~obs~ = the observed negative Friedel structure-factor
amplitude for the derivative
Fh+~calc~ = the calculated positive Friedel structure-factor
amplitude from the heavy-atom model
Fh-~calc~ = the calculated negative Friedel structure-factor
amplitude from the heavy-atom model
sum is taken over the specified reflections
Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G.
& North, A. C. T. (1961). Proc. R. Soc. London Ser. A,
265, 15-38.
phasing_MIR_der.R_cullis_centric
Residual factor R~cullis~ for centric reflections for this
derivative.
sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ |
R~cullis~ = ----------------------------------------
sum|Fph~obs~ - Fp~obs~|
Fp~obs~ = the observed structure-factor amplitude of the native
Fph~obs~ = the observed structure-factor amplitude of the
derivative
Fh~calc~ = the calculated structure-factor amplitude from the
heavy-atom model
sum is taken over the specified reflections
Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G.
& North, A. C. T. (1961). Proc. R. Soc. London Ser. A,
265, 15-38.
phasing_MIR_der.d_res_high
The lowest value for the interplanar spacings for the
reflection data used for this derivative. This is called the
highest resolution.
phasing_MIR_der.d_res_low
The highest value for the interplanar spacings for the
reflection data used for this derivative. This is called the
lowest resolution.
phasing_MIR_der.der_set_id
The data set that was treated as the derivative in this
experiment.
This data item is a pointer to attribute id in category phasing_set in the
PHASING_SET category.
phasing_MIR_der.details
A description of special aspects of this derivative, its data,
its solution or its use in phasing.
phasing_MIR_der.native_set_id
The data set that was treated as the native in this
experiment.
This data item is a pointer to attribute id in category phasing_set in the
PHASING_SET category.
phasing_MIR_der.number_of_sites
The number of heavy-atom sites in this derivative.
phasing_MIR_der.pdbx_R_cullis
record R_cullis for each derivative.
phasing_MIR_der.pdbx_R_kraut
record R_kraut obtained from all data data for each derivative.
phasing_MIR_der.pdbx_R_kraut_acentric
record R_kraut obtained from acentric data for each derivative.
phasing_MIR_der.pdbx_R_kraut_centric
record R_kraut obtained from centric data for each derivative.
phasing_MIR_der.pdbx_fom
record figure of merit obtained from all data for
each derivative.
phasing_MIR_der.pdbx_fom_acentric
record figure of merit obtained from acentric data for
each derivative.
phasing_MIR_der.pdbx_fom_centric
record figure of merit obtained from centric data for
each derivative.
phasing_MIR_der.pdbx_loc
record lack of closure obtained from all data for
each derivative.
phasing_MIR_der.pdbx_loc_acentric
record lack of closure obtained from acentric data for
each derivative.
phasing_MIR_der.pdbx_loc_centric
record lack of closure obtained from centric data for
each derivative.
phasing_MIR_der.pdbx_power
record phasing power for each derivative.
phasing_MIR_der.pdbx_reflns
record number of reflections used for each derivative.
phasing_MIR_der.power_acentric
The mean phasing power P for acentric reflections for this
derivative.
sum|Fh~calc~^2^|
P = (----------------------------)^1/2^
sum|Fph~obs~ - Fph~calc~|^2^
Fph~obs~ = the observed structure-factor amplitude of this
derivative
Fph~calc~ = the calculated structure-factor amplitude of this
derivative
Fh~calc~ = the calculated structure-factor amplitude from the
heavy-atom model
sum is taken over the specified reflections
phasing_MIR_der.power_centric
The mean phasing power P for centric reflections for this
derivative.
sum|Fh~calc~^2^|
P = (----------------------------)^1/2^
sum|Fph~obs~ - Fph~calc~|^2^
Fph~obs~ = the observed structure-factor amplitude of the
derivative
Fph~calc~ = the calculated structure-factor amplitude of the
derivative
Fh~calc~ = the calculated structure-factor amplitude from the
heavy-atom model
sum is taken over the specified reflections
phasing_MIR_der.reflns_acentric
The number of acentric reflections used in phasing for this
derivative.
phasing_MIR_der.reflns_anomalous
The number of anomalous reflections used in phasing for this
derivative.
phasing_MIR_der.reflns_centric
The number of centric reflections used in phasing for this
derivative.
phasing_MIR_der.reflns_criteria
Criteria used to limit the reflections used in the phasing
calculations.
> 4 \s(I)
phasing_MIR_der.id
The value of attribute id in category phasing_MIR_der must uniquely identify
a record in the PHASING_MIR_DER list.
Note that this item need not be a number; it can be any unique
identifier.
KAu(CN)2
K2HgI4_anom
K2HgI4_iso
phasing_MIR_der_refln
Data items in the PHASING_MIR_DER_REFLN category record details
about the calculated structure factors obtained in an MIR
phasing experiment.
This list may contain information from a number of different
derivatives; attribute der_id in category phasing_MIR_der_refln indicates to which
derivative a given record corresponds. (A derivative in this
context does not necessarily equate with a data set; see the
definition of the PHASING_MIR_DER category for a
discussion of the meaning of derivative.)
It is not necessary for the data items describing the measured
value of F to appear in this list, as they will be
given in the PHASING_SET_REFLN category. However, these
items can also be listed here for completeness.
Example 1 - based on laboratory records for the 6,1,25 reflection
of an Hg/Pt derivative of protein NS1.
<PDBx:phasing_MIR_der_reflnCategory>
<PDBx:phasing_MIR_der_refln der_id="HGPT1" index_h="6" index_k="1" index_l="25" set_id="NS1-96">
<PDBx:F_calc_au>106.66</PDBx:F_calc_au>
<PDBx:F_meas_au>204.67</PDBx:F_meas_au>
<PDBx:F_meas_sigma>6.21</PDBx:F_meas_sigma>
<PDBx:HL_A_iso>-3.15</PDBx:HL_A_iso>
<PDBx:HL_B_iso>-0.76</PDBx:HL_B_iso>
<PDBx:HL_C_iso>0.65</PDBx:HL_C_iso>
<PDBx:HL_D_iso>0.23</PDBx:HL_D_iso>
<PDBx:phase_calc>194.48</PDBx:phase_calc>
</PDBx:phasing_MIR_der_refln>
</PDBx:phasing_MIR_der_reflnCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
1
phasing_MIR_der_reflnCategory
This property indicates that datablock
has a category element phasing_MIR_der_refln.
phasing_MIR_der_reflnItem
Abstract Datatype property for phasing_MIR_der_refln items.
reference_to_phasing_MIR_der_refln
cross-reference to phasing_MIR_der_refln
phasing_MIR_der_refln.F_calc
The calculated value of the structure factor for this derivative,
in electrons.
phasing_MIR_der_refln.F_calc_au
The calculated value of the structure factor for this derivative,
in arbitrary units.
phasing_MIR_der_refln.F_meas
The measured value of the structure factor for this derivative,
in electrons.
phasing_MIR_der_refln.F_meas_au
The measured value of the structure factor for this derivative,
in arbitrary units.
phasing_MIR_der_refln.F_meas_sigma
The standard uncertainty (estimated standard deviation)
of attribute F_meas in category phasing_MIR_der_refln, in electrons.
phasing_MIR_der_refln.F_meas_sigma_au
The standard uncertainty (estimated standard deviation)
of attribute F_meas_au in category phasing_MIR_der_refln, in arbitrary units.
phasing_MIR_der_refln.HL_A_iso
The isomorphous Hendrickson-Lattman coefficient A~iso~ for this
reflection for this derivative.
-2.0 * (Fp~obs~^2^ + Fh~calc~^2^ - Fph~obs~^2^)
* Fp~obs~ * cos(alphah~calc~)
A~iso~ = -----------------------------------------------
E^2^
E = (Fph~obs~ - Fp~obs~ - Fh~calc~)^2^
for centric reflections
= [(Fph~obs~ - Fp~obs~) * 2^1/2^ - Fh~calc~]^2^
for acentric reflections
Fp~obs~ = the observed structure-factor amplitude of the
native
Fph~obs~ = the observed structure-factor amplitude of the
derivative
Fh~calc~ = the calculated structure-factor amplitude
from the heavy-atom model
alphah~calc~ = the calculated phase from the heavy-atom model
This coefficient appears in the expression for the phase
probability of each isomorphous derivative:
P~i~(alpha) = exp[k + A * cos(alpha) + B * sin(alpha)
+ C * cos(2 * alpha) + D * sin(2 * alpha)]
Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta
Cryst. B26, 136-143.
phasing_MIR_der_refln.HL_B_iso
The isomorphous Hendrickson-Lattman coefficient B~iso~ for this
reflection for this derivative.
-2.0 * (Fp~obs~^2^ + Fh~calc~^2^ - Fph~obs~^2^)
* Fp~obs~ * sin(alphah~calc~)
B~iso~ = -----------------------------------------------
E^2^
E = (Fph~obs~ - Fp~obs~ - Fh~calc~)^2^
for centric reflections
= [(Fph~obs~ - Fp~obs~) * 2^1/2^ - Fh~calc~]^2^
for acentric reflections
Fp~obs~ = the observed structure-factor amplitude of the
native
Fph~obs~ = the observed structure-factor amplitude of the
derivative
Fh~calc~ = the calculated structure-factor amplitude
from the heavy-atom model
alphah~calc~ = the phase calculated from the heavy-atom model
This coefficient appears in the expression for the phase
probability of each isomorphous derivative:
P~i~(alpha) = exp[k + A * cos(alpha) + B * sin(alpha)
+ C * cos(2 * alpha) + D * sin(2 * alpha)]
Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta
Cryst. B26, 136-143.
phasing_MIR_der_refln.HL_C_iso
The isomorphous Hendrickson-Lattman coefficient C~iso~ for this
reflection for this derivative.
-Fp~obs~^2^ * [sin(alphah~calc~)^2^
- cos(alphah~calc~)^2^]
C~iso~ = ------------------------------------
E^2^
E = (Fph~obs~ - Fp~obs~ - Fh~calc~)^2^
for centric reflections
= [(Fph~obs~ - Fp~obs~) * 2^1/2^ - Fh~calc~]^2^
for acentric reflections
Fp~obs~ = the observed structure-factor amplitude of the
native
Fph~obs~ = the observed structure-factor amplitude of the
derivative
Fh~calc~ = the calculated structure-factor amplitude
from the heavy-atom model
alphah~calc~ = the phase calculated from the heavy-atom model
This coefficient appears in the expression for the phase
probability of each isomorphous derivative:
P~i~(alpha) = exp[k + A * cos(alpha) + B * sin(alpha)
+ C * cos(2 * alpha) + D * sin(2 * alpha)]
Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta
Cryst. B26, 136-143.
phasing_MIR_der_refln.HL_D_iso
The isomorphous Hendrickson-Lattman coefficient D~iso~ for this
reflection for this derivative.
-2.0 * Fp~obs~^2^ * sin(alphah~calc~)^2^
* cos(alphah~calc~)^2^
D~iso~ = ----------------------------------------
E^2^
E = (Fph~obs~ - Fp~obs~ - Fh~calc~)^2^
for centric reflections
= [(Fph~obs~ - Fp~obs~) * 2^1/2^ - Fh~calc~]^2^
for acentric reflections
Fp~obs~ = the observed structure-factor amplitude of the
native
Fph~obs~ = the observed structure-factor amplitude of the
derivative
Fh~calc~ = the calculated structure-factor amplitude
from the heavy-atom model
alphah~calc~ = the phase calculated from the heavy-atom model
This coefficient appears in the expression for the phase
probability of each isomorphous derivative:
P~i~(alpha) = exp[k + A * cos(alpha) + B * sin(alpha)
+ C * cos(2 * alpha) + D * sin(2 * alpha)]
Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta
Cryst. B26, 136-143.
phasing_MIR_der_refln.phase_calc
The calculated value of the structure-factor phase based on the
heavy-atom model for this derivative in degrees.
phasing_MIR_der_refln.der_id
This data item is a pointer to attribute id in category phasing_MIR_der in the
PHASING_MIR_DER category.
phasing_MIR_der_refln.index_h
Miller index h for this reflection for this derivative.
phasing_MIR_der_refln.index_k
Miller index k for this reflection for this derivative.
phasing_MIR_der_refln.index_l
Miller index l for this reflection for this derivative.
phasing_MIR_der_refln.set_id
This data item is a pointer to attribute id in category phasing_set in the
PHASING_SET category.
phasing_MIR_der_shell
Data items in the PHASING_MIR_DER_SHELL category record
statistics, broken down into shells of resolution, for an MIR
phasing experiment.
This list may contain information from a number of different
derivatives; attribute der_id in category phasing_MIR_der_shell indicates to which
derivative a given record corresponds. (A derivative in this
context does not necessarily equate with a data set; see the
definition of the PHASING_MIR_DER category for a
discussion of the meaning of derivative.)
Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem.
(1993), 268, 10728-10738]
with addition of an arbitrary low-resolution limit.
<PDBx:phasing_MIR_der_shellCategory>
<PDBx:phasing_MIR_der_shell d_res_high="8.3" d_res_low="15.0" der_id="KAu(CN)2">
<PDBx:ha_ampl>54</PDBx:ha_ampl>
<PDBx:loc>26</PDBx:loc>
</PDBx:phasing_MIR_der_shell>
<PDBx:phasing_MIR_der_shell d_res_high="6.4" d_res_low="8.3" der_id="KAu(CN)2">
<PDBx:ha_ampl>54</PDBx:ha_ampl>
<PDBx:loc>20</PDBx:loc>
</PDBx:phasing_MIR_der_shell>
<PDBx:phasing_MIR_der_shell d_res_high="5.2" d_res_low="6.4" der_id="KAu(CN)2">
<PDBx:ha_ampl>50</PDBx:ha_ampl>
<PDBx:loc>20</PDBx:loc>
</PDBx:phasing_MIR_der_shell>
<PDBx:phasing_MIR_der_shell d_res_high="4.4" d_res_low="5.2" der_id="KAu(CN)2">
<PDBx:ha_ampl>44</PDBx:ha_ampl>
<PDBx:loc>23</PDBx:loc>
</PDBx:phasing_MIR_der_shell>
<PDBx:phasing_MIR_der_shell d_res_high="3.8" d_res_low="4.4" der_id="KAu(CN)2">
<PDBx:ha_ampl>39</PDBx:ha_ampl>
<PDBx:loc>23</PDBx:loc>
</PDBx:phasing_MIR_der_shell>
<PDBx:phasing_MIR_der_shell d_res_high="3.4" d_res_low="3.8" der_id="KAu(CN)2">
<PDBx:ha_ampl>33</PDBx:ha_ampl>
<PDBx:loc>21</PDBx:loc>
</PDBx:phasing_MIR_der_shell>
<PDBx:phasing_MIR_der_shell d_res_high="3.0" d_res_low="3.4" der_id="KAu(CN)2">
<PDBx:ha_ampl>28</PDBx:ha_ampl>
<PDBx:loc>17</PDBx:loc>
</PDBx:phasing_MIR_der_shell>
<PDBx:phasing_MIR_der_shell d_res_high="3.0" d_res_low="15.0" der_id="KAu(CN)2">
<PDBx:ha_ampl>38</PDBx:ha_ampl>
<PDBx:loc>21</PDBx:loc>
</PDBx:phasing_MIR_der_shell>
<PDBx:phasing_MIR_der_shell d_res_high="8.3" d_res_low="15.0" der_id="K2HgI4">
<PDBx:ha_ampl>149</PDBx:ha_ampl>
<PDBx:loc>87</PDBx:loc>
</PDBx:phasing_MIR_der_shell>
<PDBx:phasing_MIR_der_shell d_res_high="6.4" d_res_low="8.3" der_id="K2HgI4">
<PDBx:ha_ampl>121</PDBx:ha_ampl>
<PDBx:loc>73</PDBx:loc>
</PDBx:phasing_MIR_der_shell>
<PDBx:phasing_MIR_der_shell d_res_high="5.2" d_res_low="6.4" der_id="K2HgI4">
<PDBx:ha_ampl>95</PDBx:ha_ampl>
<PDBx:loc>61</PDBx:loc>
</PDBx:phasing_MIR_der_shell>
<PDBx:phasing_MIR_der_shell d_res_high="4.4" d_res_low="5.2" der_id="K2HgI4">
<PDBx:ha_ampl>80</PDBx:ha_ampl>
<PDBx:loc>60</PDBx:loc>
</PDBx:phasing_MIR_der_shell>
<PDBx:phasing_MIR_der_shell d_res_high="3.8" d_res_low="4.4" der_id="K2HgI4">
<PDBx:ha_ampl>73</PDBx:ha_ampl>
<PDBx:loc>63</PDBx:loc>
</PDBx:phasing_MIR_der_shell>
<PDBx:phasing_MIR_der_shell d_res_high="3.4" d_res_low="3.8" der_id="K2HgI4">
<PDBx:ha_ampl>68</PDBx:ha_ampl>
<PDBx:loc>57</PDBx:loc>
</PDBx:phasing_MIR_der_shell>
<PDBx:phasing_MIR_der_shell d_res_high="3.0" d_res_low="3.4" der_id="K2HgI4">
<PDBx:ha_ampl>63</PDBx:ha_ampl>
<PDBx:loc>46</PDBx:loc>
</PDBx:phasing_MIR_der_shell>
<PDBx:phasing_MIR_der_shell d_res_high="3.0" d_res_low="15.0" der_id="K2HgI4">
<PDBx:ha_ampl>79</PDBx:ha_ampl>
<PDBx:loc>58</PDBx:loc>
</PDBx:phasing_MIR_der_shell>
<PDBx:phasing_MIR_der_shell d_res_high="8.3" d_res_low="15.0" der_id="K3IrCl6">
<PDBx:ha_ampl>33</PDBx:ha_ampl>
<PDBx:loc>27</PDBx:loc>
</PDBx:phasing_MIR_der_shell>
<PDBx:phasing_MIR_der_shell d_res_high="6.4" d_res_low="8.3" der_id="K3IrCl6">
<PDBx:ha_ampl>40</PDBx:ha_ampl>
<PDBx:loc>23</PDBx:loc>
</PDBx:phasing_MIR_der_shell>
<PDBx:phasing_MIR_der_shell d_res_high="5.2" d_res_low="6.4" der_id="K3IrCl6">
<PDBx:ha_ampl>31</PDBx:ha_ampl>
<PDBx:loc>22</PDBx:loc>
</PDBx:phasing_MIR_der_shell>
<PDBx:phasing_MIR_der_shell d_res_high="4.4" d_res_low="5.2" der_id="K3IrCl6">
<PDBx:ha_ampl>27</PDBx:ha_ampl>
<PDBx:loc>23</PDBx:loc>
</PDBx:phasing_MIR_der_shell>
<PDBx:phasing_MIR_der_shell d_res_high="3.8" d_res_low="4.4" der_id="K3IrCl6">
<PDBx:ha_ampl>22</PDBx:ha_ampl>
<PDBx:loc>23</PDBx:loc>
</PDBx:phasing_MIR_der_shell>
<PDBx:phasing_MIR_der_shell d_res_high="3.4" d_res_low="3.8" der_id="K3IrCl6">
<PDBx:ha_ampl>19</PDBx:ha_ampl>
<PDBx:loc>20</PDBx:loc>
</PDBx:phasing_MIR_der_shell>
<PDBx:phasing_MIR_der_shell d_res_high="3.0" d_res_low="3.4" der_id="K3IrCl6">
<PDBx:ha_ampl>16</PDBx:ha_ampl>
<PDBx:loc>20</PDBx:loc>
</PDBx:phasing_MIR_der_shell>
<PDBx:phasing_MIR_der_shell d_res_high="3.0" d_res_low="15.0" der_id="K3IrCl6">
<PDBx:ha_ampl>23</PDBx:ha_ampl>
<PDBx:loc>21</PDBx:loc>
</PDBx:phasing_MIR_der_shell>
</PDBx:phasing_MIR_der_shellCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
phasing_MIR_der_shellCategory
This property indicates that datablock
has a category element phasing_MIR_der_shell.
phasing_MIR_der_shellItem
Abstract Datatype property for phasing_MIR_der_shell items.
reference_to_phasing_MIR_der_shell
cross-reference to phasing_MIR_der_shell
phasing_MIR_der_shell.R_cullis
Residual factor R~cullis~ for centric reflections for this
derivative in this shell.
sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ |
R~cullis~ = ----------------------------------------
sum|Fph~obs~ - Fp~obs~|
Fp~obs~ = the observed structure-factor amplitude of the native
Fph~obs~ = the observed structure-factor amplitude of the
derivative
Fh~calc~ = the calculated structure-factor amplitude from the
heavy-atom model
sum is taken over the specified reflections
Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G.
& North, A. C. T. (1961). Proc. R. Soc. London Ser. A,
265, 15-38.
phasing_MIR_der_shell.R_kraut
Residual factor R~kraut~ for general reflections for this
derivative in this shell.
sum|Fph~obs~ - Fph~calc~|
R~kraut~ = -------------------------
sum|Fph~obs~|
Fph~obs~ = the observed structure-factor amplitude of the
derivative
Fph~calc~ = the calculated structure-factor amplitude of the
derivative
sum is taken over the specified reflections
Ref: Kraut, J., Sieker, L. C., High, D. F. & Freer, S. T.
(1962). Proc. Natl Acad. Sci. USA, 48, 1417-1424.
phasing_MIR_der_shell.fom
The mean value of the figure of merit m for reflections for this
derivative in this shell.
int P~alpha~ exp(i*alpha) dalpha
m = --------------------------------
int P~alpha~ dalpha
P~alpha~ = the probability that the phase angle alpha is correct
int is taken over the range alpha = 0 to 2 pi.
phasing_MIR_der_shell.ha_ampl
The mean heavy-atom amplitude for reflections for this
derivative in this shell.
phasing_MIR_der_shell.loc
The mean lack-of-closure error loc for reflections for this
derivative in this shell.
loc = sum|Fph~obs~ - Fph~calc~|
Fph~obs~ = the observed structure-factor amplitude of the
derivative
Fph~calc~ = the calculated structure-factor amplitude of the
derivative
sum is taken over the specified reflections
phasing_MIR_der_shell.pdbx_R_cullis_acentric
record R Cullis obtained from acentric data for each
derivative, but broken into resolution shells
phasing_MIR_der_shell.pdbx_R_cullis_centric
record R Cullis obtained from centric data for each
derivative, but broken into resolution shells
phasing_MIR_der_shell.pdbx_R_kraut_acentric
record R Kraut obtained from acentric data for each
derivative, but broken into resolution shells
phasing_MIR_der_shell.pdbx_R_kraut_centric
record R Kraut obtained from centric data for each
derivative, but broken into resolution shells
phasing_MIR_der_shell.pdbx_fom_acentric
record figure of merit obtained from acentric data for each
derivative, but broken into resolution shells
phasing_MIR_der_shell.pdbx_fom_centric
record figure of merit obtained from centric data for each
derivative, but broken into resolution shells
phasing_MIR_der_shell.pdbx_loc_acentric
record lack of closure obtained from acentric data for each
derivative, but broken into resolution shells
phasing_MIR_der_shell.pdbx_loc_centric
record lack of closure obtained from centric data for each
derivative, but broken into resolution shells
phasing_MIR_der_shell.pdbx_power_acentric
record phasing power obtained from acentric data for each
derivative, but broken into resolution shells
phasing_MIR_der_shell.pdbx_power_centric
record phasing power obtained from centric data for each
derivative, but broken into resolution shells
phasing_MIR_der_shell.pdbx_reflns_acentric
record number of acentric reflections used for phasing for each
derivative, but broken into resolution shells
phasing_MIR_der_shell.pdbx_reflns_centric
record number of centric reflections used for phasing for each
derivative, but broken into resolution shells
phasing_MIR_der_shell.phase
The mean of the phase values for reflections for this
derivative in this shell.
phasing_MIR_der_shell.power
The mean phasing power P for reflections for this derivative
in this shell.
sum|Fh~calc~^2^|
P = (----------------------------)^1/2^
sum|Fph~obs~ - Fph~calc~|^2^
Fph~obs~ = the observed structure-factor amplitude of the
derivative
Fph~calc~ = the calculated structure-factor amplitude of the
derivative
Fh~calc~ = the calculated structure-factor amplitude from the
heavy-atom model
sum is taken over the specified reflections
phasing_MIR_der_shell.reflns
The number of reflections in this shell.
phasing_MIR_der_shell.d_res_high
The lowest value for the interplanar spacings for the
reflection data for this derivative in this shell. This is called
the highest resolution.
phasing_MIR_der_shell.d_res_low
The highest value for the interplanar spacings for the
reflection data for this derivative in this shell. This is called
the lowest resolution.
phasing_MIR_der_shell.der_id
This data item is a pointer to attribute id in category phasing_MIR_der in the
PHASING_MIR_DER category.
phasing_MIR_der_site
Data items in the PHASING_MIR_DER_SITE category record details
about the heavy-atom sites in an MIR phasing experiment.
This list may contain information from a number of different
derivatives; attribute der_id in category phasing_MIR_der_site indicates to which
derivative a given record corresponds. (A derivative in this
context does not necessarily equate with a data set; see the
definition of the PHASING_MIR_DER category for a
discussion of the meaning of derivative.)
Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem.
(1993), 268, 10728-10738]
with occupancies converted from electrons to fractional.
<PDBx:phasing_MIR_der_siteCategory>
<PDBx:phasing_MIR_der_site der_id="KAu(CN)2" id="1">
<PDBx:B_iso>33.0</PDBx:B_iso>
<PDBx:atom_type_symbol>Au</PDBx:atom_type_symbol>
<PDBx:fract_x>0.082</PDBx:fract_x>
<PDBx:fract_y>0.266</PDBx:fract_y>
<PDBx:fract_z>0.615</PDBx:fract_z>
<PDBx:occupancy>0.40</PDBx:occupancy>
</PDBx:phasing_MIR_der_site>
<PDBx:phasing_MIR_der_site der_id="KAu(CN)2" id="2">
<PDBx:B_iso>25.9</PDBx:B_iso>
<PDBx:atom_type_symbol>Au</PDBx:atom_type_symbol>
<PDBx:fract_x>0.607</PDBx:fract_x>
<PDBx:fract_y>0.217</PDBx:fract_y>
<PDBx:fract_z>0.816</PDBx:fract_z>
<PDBx:occupancy>0.03</PDBx:occupancy>
</PDBx:phasing_MIR_der_site>
<PDBx:phasing_MIR_der_site der_id="KAu(CN)2" id="3">
<PDBx:B_iso>15.7</PDBx:B_iso>
<PDBx:atom_type_symbol>Au</PDBx:atom_type_symbol>
<PDBx:fract_x>0.263</PDBx:fract_x>
<PDBx:fract_y>0.782</PDBx:fract_y>
<PDBx:fract_z>0.906</PDBx:fract_z>
<PDBx:occupancy>0.02</PDBx:occupancy>
</PDBx:phasing_MIR_der_site>
<PDBx:phasing_MIR_der_site der_id="K2HgI4" id="1">
<PDBx:B_iso>33.7</PDBx:B_iso>
<PDBx:atom_type_symbol>Hg</PDBx:atom_type_symbol>
<PDBx:fract_x>0.048</PDBx:fract_x>
<PDBx:fract_y>0.286</PDBx:fract_y>
<PDBx:fract_z>0.636</PDBx:fract_z>
<PDBx:occupancy>0.63</PDBx:occupancy>
</PDBx:phasing_MIR_der_site>
<PDBx:phasing_MIR_der_site der_id="K2HgI4" id="2">
<PDBx:B_iso>36.7</PDBx:B_iso>
<PDBx:atom_type_symbol>Hg</PDBx:atom_type_symbol>
<PDBx:fract_x>0.913</PDBx:fract_x>
<PDBx:fract_y>0.768</PDBx:fract_y>
<PDBx:fract_z>0.889</PDBx:fract_z>
<PDBx:occupancy>0.34</PDBx:occupancy>
</PDBx:phasing_MIR_der_site>
<PDBx:phasing_MIR_der_site der_id="K2HgI4" id="3">
<PDBx:B_iso>24.2</PDBx:B_iso>
<PDBx:atom_type_symbol>Hg</PDBx:atom_type_symbol>
<PDBx:fract_x>0.974</PDBx:fract_x>
<PDBx:fract_y>0.455</PDBx:fract_y>
<PDBx:fract_z>0.974</PDBx:fract_z>
<PDBx:occupancy>0.23</PDBx:occupancy>
</PDBx:phasing_MIR_der_site>
<PDBx:phasing_MIR_der_site der_id="K2HgI4" id="4">
<PDBx:B_iso>14.7</PDBx:B_iso>
<PDBx:atom_type_symbol>Hg</PDBx:atom_type_symbol>
<PDBx:fract_x>0.903</PDBx:fract_x>
<PDBx:fract_y>0.836</PDBx:fract_y>
<PDBx:fract_z>0.859</PDBx:fract_z>
<PDBx:occupancy>0.28</PDBx:occupancy>
</PDBx:phasing_MIR_der_site>
<PDBx:phasing_MIR_der_site der_id="K2HgI4" id="5">
<PDBx:B_iso>6.4</PDBx:B_iso>
<PDBx:atom_type_symbol>Hg</PDBx:atom_type_symbol>
<PDBx:fract_x>0.489</PDBx:fract_x>
<PDBx:fract_y>0.200</PDBx:fract_y>
<PDBx:fract_z>0.885</PDBx:fract_z>
<PDBx:occupancy>0.07</PDBx:occupancy>
</PDBx:phasing_MIR_der_site>
<PDBx:phasing_MIR_der_site der_id="K2HgI4" id="6">
<PDBx:B_iso>32.9</PDBx:B_iso>
<PDBx:atom_type_symbol>Hg</PDBx:atom_type_symbol>
<PDBx:fract_x>0.162</PDBx:fract_x>
<PDBx:fract_y>0.799</PDBx:fract_y>
<PDBx:fract_z>0.889</PDBx:fract_z>
<PDBx:occupancy>0.07</PDBx:occupancy>
</PDBx:phasing_MIR_der_site>
<PDBx:phasing_MIR_der_site der_id="K3IrCl6" id="1">
<PDBx:B_iso>40.8</PDBx:B_iso>
<PDBx:atom_type_symbol>Ir</PDBx:atom_type_symbol>
<PDBx:fract_x>0.209</PDBx:fract_x>
<PDBx:fract_y>0.739</PDBx:fract_y>
<PDBx:fract_z>0.758</PDBx:fract_z>
<PDBx:occupancy>0.26</PDBx:occupancy>
</PDBx:phasing_MIR_der_site>
<PDBx:phasing_MIR_der_site der_id="K3IrCl6" id="2">
<PDBx:B_iso>24.9</PDBx:B_iso>
<PDBx:atom_type_symbol>Ir</PDBx:atom_type_symbol>
<PDBx:fract_x>0.279</PDBx:fract_x>
<PDBx:fract_y>0.613</PDBx:fract_y>
<PDBx:fract_z>0.752</PDBx:fract_z>
<PDBx:occupancy>0.05</PDBx:occupancy>
</PDBx:phasing_MIR_der_site>
</PDBx:phasing_MIR_der_siteCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
phasing_MIR_der_siteCategory
This property indicates that datablock
has a category element phasing_MIR_der_site.
phasing_MIR_der_siteItem
Abstract Datatype property for phasing_MIR_der_site items.
reference_to_phasing_MIR_der_site
cross-reference to phasing_MIR_der_site
phasing_MIR_der_site.B_iso
Isotropic displacement parameter for this heavy-atom site in this
derivative.
phasing_MIR_der_site.B_iso_esd
The standard uncertainty (estimated standard deviation)
of attribute B_iso in category phasing_MIR_der_site.
phasing_MIR_der_site.Cartn_x
The x coordinate of this heavy-atom position in this derivative
specified as orthogonal angstroms. The orthogonal Cartesian axes
are related to the cell axes as specified by the description
given in attribute Cartn_transform_axes in category atom_sites.
phasing_MIR_der_site.Cartn_x_esd
The standard uncertainty (estimated standard deviation)
of attribute Cartn_x in category phasing_MIR_der_site.
phasing_MIR_der_site.Cartn_y
The y coordinate of this heavy-atom position in this derivative
specified as orthogonal angstroms. The orthogonal Cartesian axes
are related to the cell axes as specified by the description
given in attribute Cartn_transform_axes in category atom_sites.
phasing_MIR_der_site.Cartn_y_esd
The standard uncertainty (estimated standard deviation)
of attribute Cartn_y in category phasing_MIR_der_site.
phasing_MIR_der_site.Cartn_z
The z coordinate of this heavy-atom position in this derivative
specified as orthogonal angstroms. The orthogonal Cartesian axes
are related to the cell axes as specified by the description
given in attribute Cartn_transform_axes in category atom_sites.
phasing_MIR_der_site.Cartn_z_esd
The standard uncertainty (estimated standard deviation)
of attribute Cartn_z in category phasing_MIR_der_site.
phasing_MIR_der_site.atom_type_symbol
This data item is a pointer to attribute symbol in category atom_type in the
ATOM_TYPE category.
The scattering factors referenced via this data item should be
those used in the refinement of the heavy-atom data; in some
cases this is the scattering factor for the single heavy
atom, in other cases these are the scattering factors for an
atomic cluster.
phasing_MIR_der_site.details
A description of special aspects of the derivative site.
binds to His 117
minor site obtained from difference Fourier
same as site 2 in the K2HgI4 derivative
phasing_MIR_der_site.fract_x
The x coordinate of this heavy-atom position in this derivative
specified as a fraction of attribute length_a in category cell.
phasing_MIR_der_site.fract_x_esd
The standard uncertainty (estimated standard deviation)
of attribute fract_x in category phasing_MIR_der_site.
phasing_MIR_der_site.fract_y
The y coordinate of this heavy-atom position in this derivative
specified as a fraction of attribute length_b in category cell.
phasing_MIR_der_site.fract_y_esd
The standard uncertainty (estimated standard deviation)
of attribute fract_y in category phasing_MIR_der_site.
phasing_MIR_der_site.fract_z
The z coordinate of this heavy-atom position in this derivative
specified as a fraction of attribute length_c in category cell.
phasing_MIR_der_site.fract_z_esd
The standard uncertainty (estimated standard deviation)
of attribute fract_z in category phasing_MIR_der_site.
phasing_MIR_der_site.occupancy
The fraction of the atom type present at this heavy-atom site
in a given derivative. The sum of the occupancies of all the
atom types at this site may not significantly exceed 1.0 unless
it is a dummy site.
phasing_MIR_der_site.occupancy_anom
The relative anomalous occupancy of the atom type
present at this heavy-atom site in a given derivative.
This atom occupancy will probably be on an arbitrary scale.
phasing_MIR_der_site.occupancy_anom_su
The standard uncertainty (estimated standard deviation) of
attribute occupancy_anom in category phasing_MIR_der_site.
phasing_MIR_der_site.occupancy_iso
The relative real isotropic occupancy of the atom type
present at this heavy-atom site in a given derivative.
This atom occupancy will probably be on an arbitrary scale.
phasing_MIR_der_site.occupancy_iso_su
The standard uncertainty (estimated standard deviation) of
attribute occupancy_iso in category phasing_MIR_der_site.
phasing_MIR_der_site.der_id
This data item is a pointer to attribute id in category phasing_MIR_der in the
PHASING_MIR_DER category.
phasing_MIR_der_site.id
The value of attribute id in category phasing_MIR_der_site must uniquely identify each
site in each derivative in the PHASING_MIR_DER_SITE list.
The atom identifiers need not be unique over all sites in all
derivatives; they need only be unique for each site in each
derivative.
Note that this item need not be a number; it can be any unique
identifier.
phasing_MIR_shell
Data items in the PHASING_MIR_SHELL category record statistics
for an isomorphous replacement phasing experiment.broken
down into shells of resolution.
Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem.
(1993), 268, 10728-10738]
with addition of an arbitrary low-resolution limit.
<PDBx:phasing_MIR_shellCategory>
<PDBx:phasing_MIR_shell d_res_high="8.3" d_res_low="15.0">
<PDBx:FOM>0.69</PDBx:FOM>
<PDBx:reflns>80</PDBx:reflns>
</PDBx:phasing_MIR_shell>
<PDBx:phasing_MIR_shell d_res_high="6.4" d_res_low="8.3">
<PDBx:FOM>0.73</PDBx:FOM>
<PDBx:reflns>184</PDBx:reflns>
</PDBx:phasing_MIR_shell>
<PDBx:phasing_MIR_shell d_res_high="5.2" d_res_low="6.4">
<PDBx:FOM>0.72</PDBx:FOM>
<PDBx:reflns>288</PDBx:reflns>
</PDBx:phasing_MIR_shell>
<PDBx:phasing_MIR_shell d_res_high="4.4" d_res_low="5.2">
<PDBx:FOM>0.65</PDBx:FOM>
<PDBx:reflns>406</PDBx:reflns>
</PDBx:phasing_MIR_shell>
<PDBx:phasing_MIR_shell d_res_high="3.8" d_res_low="4.4">
<PDBx:FOM>0.54</PDBx:FOM>
<PDBx:reflns>554</PDBx:reflns>
</PDBx:phasing_MIR_shell>
<PDBx:phasing_MIR_shell d_res_high="3.4" d_res_low="3.8">
<PDBx:FOM>0.53</PDBx:FOM>
<PDBx:reflns>730</PDBx:reflns>
</PDBx:phasing_MIR_shell>
<PDBx:phasing_MIR_shell d_res_high="3.0" d_res_low="3.4">
<PDBx:FOM>0.50</PDBx:FOM>
<PDBx:reflns>939</PDBx:reflns>
</PDBx:phasing_MIR_shell>
</PDBx:phasing_MIR_shellCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
phasing_MIR_shellCategory
This property indicates that datablock
has a category element phasing_MIR_shell.
phasing_MIR_shellItem
Abstract Datatype property for phasing_MIR_shell items.
reference_to_phasing_MIR_shell
cross-reference to phasing_MIR_shell
phasing_MIR_shell.FOM
The mean value of the figure of merit m for reflections in this
shell.
int P~alpha~ exp(i*alpha) dalpha
m = --------------------------------
int P~alpha~ dalpha
P~alpha~ = the probability that the phase angle alpha is correct
the integral is taken over the range alpha = 0 to 2 pi.
phasing_MIR_shell.FOM_acentric
The mean value of the figure of merit m for acentric reflections
in this shell.
int P~alpha~ exp(i*alpha) dalpha
m = --------------------------------
int P~alpha~ dalpha
P~a~ = the probability that the phase angle a is correct
the integral is taken over the range alpha = 0 to 2 pi.
phasing_MIR_shell.FOM_centric
The mean value of the figure of merit m for centric reflections
in this shell.
int P~alpha~ exp(i*alpha) dalpha
m = --------------------------------
int P~alpha~ dalpha
P~a~ = the probability that the phase angle a is correct
the integral is taken over the range alpha = 0 to 2 pi.
phasing_MIR_shell.R_cullis
Residual factor R~cullis~ for centric reflections in this shell.
sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ |
R~cullis~ = ----------------------------------------
sum|Fph~obs~ - Fp~obs~|
Fp~obs~ = the observed structure-factor amplitude of the native
Fph~obs~ = the observed structure-factor amplitude of the
derivative
Fh~calc~ = the calculated structure-factor amplitude from the
heavy-atom model
sum is taken over the specified reflections
Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G.
& North, A. C. T. (1961). Proc. R. Soc. London Ser. A,
265, 15-38.
phasing_MIR_shell.R_kraut
Residual factor R~kraut~ for general reflections in this shell.
sum|Fph~obs~ - Fph~calc~|
R~kraut~ = -------------------------
sum|Fph~obs~|
Fph~obs~ = the observed structure-factor amplitude of the
derivative
Fph~calc~ = the calculated structure-factor amplitude of the
derivative
sum is taken over the specified reflections
Ref: Kraut, J., Sieker, L. C., High, D. F. & Freer, S. T.
(1962). Proc. Natl Acad. Sci. USA, 48, 1417-1424.
phasing_MIR_shell.loc
The mean lack-of-closure error loc for reflections in this shell.
loc = sum|Fph~obs~ - Fph~calc~|
Fph~obs~ = the observed structure-factor amplitude of the
derivative
Fph~calc~ = the calculated structure-factor amplitude of the
derivative
sum is taken over the specified reflections
phasing_MIR_shell.mean_phase
The mean of the phase values for all reflections in this shell.
phasing_MIR_shell.pdbx_R_cullis_acentric
record R_Cullis from from acentric reflection for each shell.
phasing_MIR_shell.pdbx_R_cullis_centric
record R_Cullis from from centric reflection for each shell.
phasing_MIR_shell.pdbx_R_kraut_acentric
record R_kraut from from acentric reflection for each shell.
phasing_MIR_shell.pdbx_R_kraut_centric
record R_Kraut from from centric reflection for each shell.
phasing_MIR_shell.pdbx_loc_acentric
record lack of closure from acentric reflection for each shell.
phasing_MIR_shell.pdbx_loc_centric
record lack of closure from centric reflection for each shell.
phasing_MIR_shell.pdbx_power_acentric
record phasing power from acentric reflection for each shell.
phasing_MIR_shell.pdbx_power_centric
record phasing power from centric reflection for each shell.
phasing_MIR_shell.power
The mean phasing power P for reflections in this shell.
sum|Fh~calc~^2^|
P = (----------------------------)^1/2^
sum|Fph~obs~ - Fph~calc~|^2^
Fph~obs~ = the observed structure-factor amplitude of the
derivative
Fph~calc~ = the calculated structure-factor amplitude of the
derivative
Fh~calc~ = the calculated structure-factor amplitude from the
heavy-atom model
sum is taken over the specified reflections
phasing_MIR_shell.reflns
The number of reflections in this shell.
phasing_MIR_shell.reflns_acentric
The number of acentric reflections in this shell.
phasing_MIR_shell.reflns_anomalous
The number of anomalous reflections in this shell.
phasing_MIR_shell.reflns_centric
The number of centric reflections in this shell.
phasing_MIR_shell.d_res_high
The lowest value for the interplanar spacings for the
reflection data in this shell. This is called the highest
resolution. Note that the resolution limits of shells in
the items attribute d_res_high in category phasing_MIR_shell and
attribute d_res_low in category phasing_MIR_shell are independent of the resolution
limits of shells in the items attribute d_res_high in category reflns_shell and
attribute d_res_low in category reflns_shell.
phasing_MIR_shell.d_res_low
The highest value for the interplanar spacings for the
reflection data in this shell. This is called the lowest
resolution. Note that the resolution limits of shells in the
items attribute d_res_high in category phasing_MIR_shell and
attribute d_res_low in category phasing_MIR_shell are independent of the resolution
limits of shells in the items attribute d_res_high in category reflns_shell and
attribute d_res_low in category reflns_shell.
phasing_averaging
Data items in the PHASING_AVERAGING category record details
about the phasing of the structure where methods involving
averaging of multiple observations of the molecule in the
asymmetric unit are involved.
Example 1 - hypothetical example.
<PDBx:phasing_averagingCategory>
<PDBx:phasing_averaging entry_id="EXAMHYPO">
<PDBx:details> The position of the threefold axis was redetermined every
five cycles.</PDBx:details>
<PDBx:method> Iterative threefold averaging alternating with phase
extensions by 0.5 reciprocal lattice units per cycle.</PDBx:method>
</PDBx:phasing_averaging>
</PDBx:phasing_averagingCategory>
0
1
0
1
1
phasing_averagingCategory
This property indicates that datablock
has a category element phasing_averaging.
phasing_averagingItem
Abstract Datatype property for phasing_averaging items.
reference_to_phasing_averaging
cross-reference to phasing_averaging
phasing_averaging.details
A description of special aspects of the averaging process.
phasing_averaging.method
A description of the phase-averaging phasing method used to
phase this structure.
Note that this is not the computer program used, which is
described in the SOFTWARE category, but rather the method
itself.
This data item should be used to describe significant
methodological options used within the phase-averaging program.
phasing_averaging.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
phasing_isomorphous
Data items in the PHASING_ISOMORPHOUS category record details
about the phasing of the structure where a model isomorphous
to the structure being phased was used to generate the initial
phases.
Example 1 - based on PDB entry 4PHV and laboratory records for the
structure corresponding to PDB entry 4PHV.
<PDBx:phasing_isomorphousCategory>
<PDBx:phasing_isomorphous entry_id="1ABC">
<PDBx:details> The inhibitor and all solvent atoms were removed from the
parent structure before beginning refinement. All static
disorder present in the parent structure was also removed.</PDBx:details>
<PDBx:parent>PDB entry 5HVP</PDBx:parent>
</PDBx:phasing_isomorphous>
</PDBx:phasing_isomorphousCategory>
0
1
0
1
0
1
1
phasing_isomorphousCategory
This property indicates that datablock
has a category element phasing_isomorphous.
phasing_isomorphousItem
Abstract Datatype property for phasing_isomorphous items.
reference_to_phasing_isomorphous
cross-reference to phasing_isomorphous
phasing_isomorphous.details
A description of special aspects of the isomorphous phasing.
Residues 13-18 were eliminated from the
starting model as it was anticipated that
binding of the inhibitor would cause a
structural rearrangement in this part of the
structure.
phasing_isomorphous.method
A description of the isomorphous-phasing method used to
phase this structure.
Note that this is not the computer program used, which is
described in the SOFTWARE category, but rather the method
itself.
This data item should be used to describe significant
methodological options used within the isomorphous phasing
program.
Iterative threefold averaging alternating with
phase extension by 0.5 reciprocal lattice
units per cycle.
phasing_isomorphous.parent
Reference to the structure used to generate starting phases
if the structure referenced in this data block was phased
by virtue of being isomorphous to a known structure (e.g.
a mutant that crystallizes in the same space group as the
wild-type protein.)
phasing_isomorphous.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
phasing_set
Data items in the PHASING_SET category record details about
the data sets used in a phasing experiment. A given data set
may be used in a number of different ways; for instance, a
single data set could be used both as an isomorphous derivative
and as a component of a multiple-wavelength calculation. This
category establishes identifiers for each data set and permits
the archiving of a subset of experimental information for each
data set (cell constants, wavelength, temperature etc.).
This and related categories of data items are provided so that
derivative intensity and phase information can be stored in
the same data block as the information for the refined
structure.
If all the possible experimental information for each data
set (raw data sets, crystal growth conditions etc.) is to be
archived, these data items should be recorded in a separate
data block.
Example 1 - based on laboratory records for an Hg/Pt derivative of
protein NS1.
<PDBx:phasing_setCategory>
<PDBx:phasing_set id="NS1-96">
<PDBx:cell_angle_alpha>90.0</PDBx:cell_angle_alpha>
<PDBx:cell_angle_beta>90.0</PDBx:cell_angle_beta>
<PDBx:cell_angle_gamma>90.0</PDBx:cell_angle_gamma>
<PDBx:cell_length_a>38.63</PDBx:cell_length_a>
<PDBx:cell_length_b>38.63</PDBx:cell_length_b>
<PDBx:cell_length_c>82.88</PDBx:cell_length_c>
<PDBx:detector_specific>RXII</PDBx:detector_specific>
<PDBx:detector_type>image plate</PDBx:detector_type>
<PDBx:radiation_wavelength>1.5145</PDBx:radiation_wavelength>
</PDBx:phasing_set>
</PDBx:phasing_setCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
0
1
0
1
0
1
0
1
1
phasing_setCategory
This property indicates that datablock
has a category element phasing_set.
phasing_setItem
Abstract Datatype property for phasing_set items.
reference_to_phasing_set
cross-reference to phasing_set
phasing_set.cell_angle_alpha
Unit-cell angle alpha for this data set in degrees.
phasing_set.cell_angle_beta
Unit-cell angle beta for this data set in degrees.
phasing_set.cell_angle_gamma
Unit-cell angle gamma for this data set in degrees.
phasing_set.cell_length_a
Unit-cell length a for this data set in angstroms.
phasing_set.cell_length_b
Unit-cell length b for this data set in angstroms.
phasing_set.cell_length_c
Unit-cell length c for this data set in angstroms.
phasing_set.detector_specific
The particular radiation detector. In general, this will be a
manufacturer, description, model number or some combination of
these.
Siemens model x
Kodak XG
MAR Research model y
phasing_set.detector_type
The general class of the radiation detector.
multiwire
imaging plate
CCD
film
phasing_set.pdbx_d_res_high
The smallest value in angstroms for the interplanar spacings
for the reflections in this shell. This is called the highest
resolution.
phasing_set.pdbx_d_res_low
The highest value in angstroms for the interplanar spacings
for the reflections in this shell. This is called the lowest
resolution.
phasing_set.pdbx_temp_details
The value of attribute pdbx_temp_details in category phasing_set describes any
special details about the data collection temperature
for this phasing data set.
phasing_set.radiation_source_specific
The particular source of radiation. In general, this will be a
manufacturer, description, or model number (or some combination
of these) for laboratory sources and an institution name and
beamline name for synchrotron sources.
Rigaku RU200
Philips fine focus Mo
NSLS beamline X8C
phasing_set.radiation_wavelength
The mean wavelength of the radiation used to measure this
data set.
phasing_set.temp
The temperature in kelvins at which the data set was
measured.
phasing_set.id
The value of attribute id in category phasing_set must uniquely identify
a record in the PHASING_SET list.
Note that this item need not be a number; it can be any unique
identifier.
KAu(CN)2
K2HgI4
phasing_set_refln
Data items in the PHASING_SET_REFLN category record the values
of the measured structure factors used in a phasing experiment.
This list may contain information from a number of different
data sets; attribute set_id in category phasing_set_refln indicates the data set
to which a given record corresponds.
Example 1 - based on laboratory records for the 15,15,32
reflection of an Hg/Pt derivative of protein NS1.
<PDBx:phasing_set_reflnCategory>
<PDBx:phasing_set_refln index_h="15" index_k="15" index_l="32" set_id="NS1-96">
<PDBx:F_meas_au>181.79</PDBx:F_meas_au>
<PDBx:F_meas_sigma_au>3.72</PDBx:F_meas_sigma_au>
</PDBx:phasing_set_refln>
</PDBx:phasing_set_reflnCategory>
0
1
0
1
0
1
0
1
1
1
1
1
phasing_set_reflnCategory
This property indicates that datablock
has a category element phasing_set_refln.
phasing_set_reflnItem
Abstract Datatype property for phasing_set_refln items.
reference_to_phasing_set_refln
cross-reference to phasing_set_refln
phasing_set_refln.F_meas
The measured value of the structure factor for this reflection
in this data set in electrons.
phasing_set_refln.F_meas_au
The measured value of the structure factor for this reflection
in this data set in arbitrary units.
phasing_set_refln.F_meas_sigma
The standard uncertainty (estimated standard deviation)
of attribute F_meas in category phasing_set_refln in electrons.
phasing_set_refln.F_meas_sigma_au
The standard uncertainty (estimated standard deviation)
of attribute F_meas_au in category phasing_set_refln in arbitrary units.
phasing_set_refln.index_h
Miller index h of this reflection in this data set.
phasing_set_refln.index_k
Miller index k of this reflection in this data set.
phasing_set_refln.index_l
Miller index l of this reflection in this data set.
phasing_set_refln.set_id
This data item is a pointer to attribute id in category phasing_set in the
PHASING_SET category.
publ
Data items in the PUBL category are used when submitting a
manuscript for publication.
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<PDBx:publCategory>
<PDBx:publ entry_id="1ABC">
<PDBx:section_abstract> The oxazolidinone ring is a shallow envelope
conformation with the tert-butyl and iso-butyl groups
occupying trans-positions with respect to the ring. The
angles at the N atom sum to 356.2\%, indicating a very
small degree of pyramidalization at this atom. This is
consistent with electron delocalization between the N
atom and the carbonyl centre [N-C=O = 1.374(3)\%A].</PDBx:section_abstract>
<PDBx:section_title> trans-3-Benzoyl-2-(tert-butyl)-4-(iso-butyl)-
1,3-oxazolidin-5-one</PDBx:section_title>
</PDBx:publ>
</PDBx:publCategory>
Example 2 - based on C~31~H~48~N~4~O~4~, reported by Coleman, Patrick,
Andersen & Rettig [Acta Cryst. (1996), C52, 1525-1527].
<PDBx:publCategory>
<PDBx:publ entry_id="1ABC">
<PDBx:section_title> Hemiasterlin methyl ester</PDBx:section_title>
<PDBx:section_title_footnote> IUPAC name: methyl 2,5-dimethyl-4-{2-[3-methyl-
2-methylamino-3-(N-methylbenzo[b]pyrrol-
3-yl)butanamido]-3,3-dimethyl-N-methyl-
butanamido}-2-hexenoate.</PDBx:section_title_footnote>
</PDBx:publ>
</PDBx:publCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
publCategory
This property indicates that datablock
has a category element publ.
publItem
Abstract Datatype property for publ items.
reference_to_publ
cross-reference to publ
publ.contact_author
The name and address of the author submitting the manuscript and
data block. This is the person contacted by the journal
editorial staff. It is preferable to use the separate data items
_publ.contact_author_name and _publ.contact_author_address.
Professor George Ferguson
Department of Chemistry and Biochemistry
University of Guelph
Ontario
Canada
N1G 2W1
publ.contact_author_address
The address of the author submitting the manuscript and data
block. This is the person contacted by the journal editorial
staff.
Department of Chemistry and Biochemistry
University of Guelph
Ontario
Canada
N1G 2W1
publ.contact_author_email
E-mail address in a form recognizable to international networks.
The format of e-mail addresses is given in Section 3.4, Address
Specification, of Internet Message Format, RFC 2822, P. Resnick
(Editor), Network Standards Group, April 2001.
name@host.domain.country
uur5@banjo.bitnet
publ.contact_author_fax
Facsimile telephone number of the author submitting the
manuscript and data block.
The recommended style starts with the international dialing
prefix, followed by the area code in parentheses, followed by the
local number with no spaces. The earlier convention of including
the international dialing prefix in parentheses is no longer
recommended.
12(34)9477330
12()349477330
publ.contact_author_name
The name of the author submitting the manuscript and data
block. This is the person contacted by the journal editorial
staff.
Professor George Ferguson
publ.contact_author_phone
Telephone number of the author submitting the manuscript and
data block.
The recommended style starts with the international dialing
prefix, followed by the area code in parentheses, followed by the
local number and any extension number prefixed by 'x',
with no spaces. The earlier convention of including
the international dialing prefix in parentheses is no longer
recommended.
12(34)9477330
12()349477330
12(34)9477330x5543
publ.contact_letter
A letter submitted to the journal editor by the contact author.
publ.manuscript_creation
A description of the word-processor package and computer used to
create the word-processed manuscript stored as
attribute manuscript_processed in category publ.
Tex file created by FrameMaker on a Sun 3/280
publ.manuscript_processed
The full manuscript of a paper (excluding possibly the figures
and the tables) output in ASCII characters from a word processor.
Information about the generation of this data item must be
specified in the data item attribute manuscript_creation in category publ.
publ.manuscript_text
The full manuscript of a paper (excluding figures and possibly
the tables) output as standard ASCII text.
FA
FI
FO
FM
CI
CO
CM
EI
EO
EM
AD
SC
The category of paper submitted. For submission to
Acta Crystallographica Section C or
Acta Crystallographica Section E, ONLY the codes indicated
for use with these journals should be used.
publ.requested_coeditor_name
The name of the co-editor whom the authors would like to
handle the submitted manuscript.
publ.requested_journal
The name of the journal to which the manuscript is being
submitted.
publ.section_abstract
The abstract section of a manuscript if the manuscript is
submitted in parts. As an alternative see attribute manuscript_text
in category publ and attribute manuscript_processed in category publ.
publ.section_acknowledgements
The acknowledgements section of a manuscript if the manuscript is
submitted in parts. As an alternative see attribute manuscript_text
in category publ and attribute manuscript_processed in category publ.
publ.section_comment
The comment section of a manuscript if the manuscript is
submitted in parts. As an alternative see attribute manuscript_text
in category publ and attribute manuscript_processed in category publ.
publ.section_discussion
The discussion section of a manuscript if the manuscript is
submitted in parts. As an alternative see attribute manuscript_text
in category publ and attribute manuscript_processed in category publ.
publ.section_experimental
The experimental section of a manuscript if the manuscript is
submitted in parts. As an alternative see attribute manuscript_text
in category publ and attribute manuscript_processed.
in category publ The _publ.section_exptl_prep, _publ.section_exptl_solution and
attribute section_exptl_refinement in category publ items are preferred for
separating the chemical preparation, structure solution and
refinement aspects of the description of the experiment.
publ.section_exptl_prep
The experimental preparation section of a manuscript if the
manuscript is submitted in parts. As an alternative see
_publ.manuscript_text and _publ.manuscript_processed.
publ.section_exptl_refinement
The experimental refinement section of a manuscript if the
manuscript is submitted in parts. As an alternative see
_publ.manuscript_text and _publ.manuscript_processed.
publ.section_exptl_solution
The experimental solution section of a manuscript if the
manuscript is submitted in parts. As an alternative see
_publ.manuscript_text and _publ.manuscript_processed.
publ.section_figure_captions
The figure captions section of a manuscript if the manuscript is
submitted in parts. As an alternative see attribute manuscript_text
in category publ and attribute manuscript_processed in category publ.
publ.section_introduction
The introduction section of a manuscript if the manuscript is
submitted in parts. As an alternative see attribute manuscript_text
in category publ and attribute manuscript_processed in category publ.
publ.section_references
The references section of a manuscript if the manuscript is
submitted in parts. As an alternative see attribute manuscript_text
in category publ and attribute manuscript_processed in category publ.
publ.section_synopsis
The synopsis section of a manuscript if the manuscript is
submitted in parts. As an alternative see attribute manuscript_text
in category publ and attribute manuscript_processed in category publ.
publ.section_table_legends
The table legends section of a manuscript if the manuscript
is submitted in parts. As an alternative see
_publ.manuscript_text and _publ.manuscript_processed.
publ.section_title
The title of a manuscript if the manuscript is submitted in
parts. As an alternative see attribute manuscript_text in category publ and
attribute manuscript_processed in category publ.
publ.section_title_footnote
The footnote to the title of a manuscript if the manuscript
is submitted in parts. As an alternative see
_publ.manuscript_text and _publ.manuscript_processed.
publ.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
publ_author
Data items in the PUBL_AUTHOR category record details of
the authors of a manuscript submitted for publication.
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<PDBx:publ_authorCategory>
<PDBx:publ_author name="Willis, Anthony C.">
<PDBx:address> Research School of Chemistry
Australian National University
GPO Box 4
Canberra, A.C.T.
Australia 2601</PDBx:address>
</PDBx:publ_author>
</PDBx:publ_authorCategory>
0
1
0
1
0
1
0
1
1
publ_authorCategory
This property indicates that datablock
has a category element publ_author.
publ_authorItem
Abstract Datatype property for publ_author items.
reference_to_publ_author
cross-reference to publ_author
publ_author.address
The address of a publication author. If there is more than one
author this is looped with attribute name in category publ_author.
Department
Institute
Street
City and postcode
COUNTRY
publ_author.email
The e-mail address of a publication author. If there is more
than one author, this will be looped with attribute name.
in category publ_author The format of e-mail addresses is given in Section 3.4, Address
Specification, of Internet Message Format, RFC 2822, P. Resnick
(Editor), Network Standards Group, April 2001.
name@host.domain.country
bm@iucr.org
publ_author.footnote
A footnote accompanying an author's name in the list of authors
of a paper. Typically indicates sabbatical address, additional
affiliations or date of decease.
On leave from U. Western Australia
Also at Department of Biophysics
publ_author.id_iucr
Identifier in the IUCr contact database of a publication
author. This identifier may be available from the World
Directory of Crystallographers (http://wdc.iucr.org).
2985
publ_author.name
The name of a publication author. If there are multiple authors
this will be looped with attribute address in category publ_author. The family
name(s), followed by a comma and including any dynastic
components, precedes the first names or initials.
Bleary, Percival R.
O'Neil, F.K.
Van den Bossche, G.
Yang, D.-L.
Simonov, Yu.A
publ_body
Data items in the PUBL_BODY category permit the labelling of
different text sections within the body of a paper.
Note that these should not be used in a paper which has
a standard format with sections tagged by specific data names
(such as in Acta Crystallographica Section C). Typically,
each journal will supply a list of the specific items it
requires in its Notes for Authors.
Example 1 - based on a paper by R. Restori & D. Schwarzenbach
[Acta Cryst. (1996), A52, 369-378].
<PDBx:publ_bodyCategory>
<PDBx:publ_body element="section" label="1">
<PDBx:contents> X-ray diffraction from a crystalline material provides
information on the thermally and spatially averaged
electron density in the crystal...</PDBx:contents>
<PDBx:format>cif</PDBx:format>
<PDBx:title>Introduction</PDBx:title>
</PDBx:publ_body>
<PDBx:publ_body element="section" label="2">
<PDBx:contents> In the rigid-atom approximation, the dynamic electron
density of an atom is described by the convolution
product of the static atomic density and a probability
density function,
$\rho_{dyn}(\bf r) = \rho_{stat}(\bf r) * P(\bf r). \eqno(1)$</PDBx:contents>
<PDBx:format>tex</PDBx:format>
<PDBx:title>Theory</PDBx:title>
</PDBx:publ_body>
</PDBx:publ_bodyCategory>
Example 2 - based on a paper by R. J. Papoular, Y. Vekhter & P. Coppens
[Acta Cryst. (1996), A52, 397-407].
<PDBx:publ_bodyCategory>
<PDBx:publ_body element="section" label="3">
<PDBx:contents></PDBx:contents>
<PDBx:title> The two-channel method for retrieval of the deformation
electron density</PDBx:title>
</PDBx:publ_body>
<PDBx:publ_body element="subsection" label="3.1">
<PDBx:contents> As the wide dynamic range involved in the total electron
density...</PDBx:contents>
<PDBx:title>The two-channel entropy S[\D\r(r)]</PDBx:title>
</PDBx:publ_body>
<PDBx:publ_body element="subsection" label="3.2">
<PDBx:contents></PDBx:contents>
<PDBx:title>Uniform vs informative prior model densities</PDBx:title>
</PDBx:publ_body>
<PDBx:publ_body element="subsubsection" label="3.2.1">
<PDBx:contents> Straightforward algebra leads to expressions analogous
to...</PDBx:contents>
<PDBx:title>Use of uniform models</PDBx:title>
</PDBx:publ_body>
</PDBx:publ_bodyCategory>
0
1
0
1
0
1
1
1
publ_bodyCategory
This property indicates that datablock
has a category element publ_body.
publ_bodyItem
Abstract Datatype property for publ_body items.
reference_to_publ_body
cross-reference to publ_body
publ_body.contents
A text section of a paper.
ascii
cif
latex
sgml
tex
troff
Code indicating the appropriate typesetting conventions
for accented characters and special symbols in the text
section.
publ_body.title
Title of the associated section of text.
section
subsection
subsubsection
appendix
footnote
The functional role of the associated text section.
publ_body.label
Code identifying the section of text.
1
1.1
2.1.3
publ_manuscript_incl
Data items in the PUBL_MANUSCRIPT_INCL category allow
the authors of a manuscript submitted for publication to list
data names that should be added to the standard request list
used by the journal printing software.
Example 1 - hypothetical example.
<PDBx:publ_manuscript_inclCategory>
<PDBx:publ_manuscript_incl entry_id="EXAMHYPO">
<PDBx:extra_defn>yes</PDBx:extra_defn>
<PDBx:extra_info>to emphasise special sites</PDBx:extra_info>
<PDBx:extra_item>_atom_site.symmetry_multiplicity</PDBx:extra_item>
</PDBx:publ_manuscript_incl>
<PDBx:publ_manuscript_incl entry_id="EXAMHYPO">
<PDBx:extra_defn>yes</PDBx:extra_defn>
<PDBx:extra_info>rare material, unusual source</PDBx:extra_info>
<PDBx:extra_item>_chemical.compound_source</PDBx:extra_item>
</PDBx:publ_manuscript_incl>
<PDBx:publ_manuscript_incl entry_id="EXAMHYPO">
<PDBx:extra_defn>yes</PDBx:extra_defn>
<PDBx:extra_info>limited data is a problem here</PDBx:extra_info>
<PDBx:extra_item>_reflns.d_resolution_high</PDBx:extra_item>
</PDBx:publ_manuscript_incl>
<PDBx:publ_manuscript_incl entry_id="EXAMHYPO">
<PDBx:extra_defn>no</PDBx:extra_defn>
<PDBx:extra_info>unusual value for this material</PDBx:extra_info>
<PDBx:extra_item>_crystal.magnetic_permeability</PDBx:extra_item>
</PDBx:publ_manuscript_incl>
</PDBx:publ_manuscript_inclCategory>
0
1
0
1
0
1
1
publ_manuscript_inclCategory
This property indicates that datablock
has a category element publ_manuscript_incl.
publ_manuscript_inclItem
Abstract Datatype property for publ_manuscript_incl items.
reference_to_publ_manuscript_incl
cross-reference to publ_manuscript_incl
no
n
yes
y
Flags whether the corresponding data item marked for inclusion
in a journal request list is a standard CIF definition or not.
publ_manuscript_incl.extra_info
A short note indicating the reason why the author wishes the
corresponding data item marked for inclusion in the journal
request list to be published.
to emphasise very special sites
rare material from unusual source
the limited data is a problem here
a new data quantity needed here
publ_manuscript_incl.extra_item
Specifies the inclusion of specific data into a manuscript
which are not normally requested by the journal. The values
of this item are the extra data names (which MUST be enclosed
in single quotes) that will be added to the journal request list.
_atom_site.symmetry_multiplicity
_chemical.compound_source
_reflns.d_resolution_high
_crystal.magnetic_permeability
publ_manuscript_incl.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
refine
Data items in the REFINE category record details about the
structure-refinement parameters.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:refineCategory>
<PDBx:refine entry_id="5HVP" pdbx_refine_id="X-ray">
<PDBx:ls_R_factor_obs>0.176</PDBx:ls_R_factor_obs>
<PDBx:ls_number_parameters>7032</PDBx:ls_number_parameters>
<PDBx:ls_number_reflns_obs>12901</PDBx:ls_number_reflns_obs>
<PDBx:ls_number_restraints>6609</PDBx:ls_number_restraints>
<PDBx:ls_weighting_details> Sigdel model of Konnert-Hendrickson:
Sigdel: Afsig + Bfsig*(sin(theta)/lambda-1/6)
Afsig = 22.0, Bfsig = -150.0 at beginning of refinement
Afsig = 15.5, Bfsig = -50.0 at end of refinement</PDBx:ls_weighting_details>
<PDBx:ls_weighting_scheme>calc</PDBx:ls_weighting_scheme>
</PDBx:refine>
</PDBx:refineCategory>
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<PDBx:refineCategory>
<PDBx:refine entry_id="TOZ" pdbx_refine_id="X-ray">
<PDBx:details>sfls:_F_calc_weight_full_matrix</PDBx:details>
<PDBx:diff_density_max>.131</PDBx:diff_density_max>
<PDBx:diff_density_min>-.108</PDBx:diff_density_min>
<PDBx:ls_R_factor_all>.038</PDBx:ls_R_factor_all>
<PDBx:ls_R_factor_obs>.034</PDBx:ls_R_factor_obs>
<PDBx:ls_abs_structure_Flack>0</PDBx:ls_abs_structure_Flack>
<PDBx:ls_abs_structure_details> The absolute configuration was assigned to agree with the
known chirality at C3 arising from its precursor l-leucine.</PDBx:ls_abs_structure_details>
<PDBx:ls_extinction_coef>3514</PDBx:ls_extinction_coef>
<PDBx:ls_extinction_expression> Larson, A. C. (1970). "Crystallographic Computing", edited
by F. R. Ahmed. Eq. (22) p. 292. Copenhagen: Munksgaard.</PDBx:ls_extinction_expression>
<PDBx:ls_extinction_method>Zachariasen</PDBx:ls_extinction_method>
<PDBx:ls_goodness_of_fit_all>1.462</PDBx:ls_goodness_of_fit_all>
<PDBx:ls_goodness_of_fit_obs>1.515</PDBx:ls_goodness_of_fit_obs>
<PDBx:ls_hydrogen_treatment>refxyz except H332B noref</PDBx:ls_hydrogen_treatment>
<PDBx:ls_matrix_type>full</PDBx:ls_matrix_type>
<PDBx:ls_number_constraints>0</PDBx:ls_number_constraints>
<PDBx:ls_number_parameters>272</PDBx:ls_number_parameters>
<PDBx:ls_number_reflns_obs>1408</PDBx:ls_number_reflns_obs>
<PDBx:ls_number_restraints>0</PDBx:ls_number_restraints>
<PDBx:ls_shift_over_esd_max>.535</PDBx:ls_shift_over_esd_max>
<PDBx:ls_shift_over_esd_mean>.044</PDBx:ls_shift_over_esd_mean>
<PDBx:ls_structure_factor_coef>F</PDBx:ls_structure_factor_coef>
<PDBx:ls_wR_factor_all>.044</PDBx:ls_wR_factor_all>
<PDBx:ls_wR_factor_obs>.042</PDBx:ls_wR_factor_obs>
<PDBx:ls_weighting_details>w=1/(\s^2^(F)+0.0004F^2^)</PDBx:ls_weighting_details>
<PDBx:ls_weighting_scheme>calc</PDBx:ls_weighting_scheme>
</PDBx:refine>
</PDBx:refineCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
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1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
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1
0
1
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1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
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1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
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0
1
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1
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1
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1
0
1
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1
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1
refineCategory
This property indicates that datablock
has a category element refine.
refineItem
Abstract Datatype property for refine items.
reference_to_refine
cross-reference to refine
refine.B_iso_max
The maximum isotropic displacement parameter (B value)
found in the coordinate set.
refine.B_iso_mean
The mean isotropic displacement parameter (B value)
for the coordinate set.
refine.B_iso_min
The minimum isotropic displacement parameter (B value)
found in the coordinate set.
refine.aniso_B11
The [1][1] element of the matrix that defines the overall
anisotropic displacement model if one was refined for this
structure.
refine.aniso_B12
The [1][2] element of the matrix that defines the overall
anisotropic displacement model if one was refined for this
structure.
refine.aniso_B13
The [1][3] element of the matrix that defines the overall
anisotropic displacement model if one was refined for this
structure.
refine.aniso_B22
The [2][2] element of the matrix that defines the overall
anisotropic displacement model if one was refined for this
structure.
refine.aniso_B23
The [2][3] element of the matrix that defines the overall
anisotropic displacement model if one was refined for this
structure.
refine.aniso_B33
The [3][3] element of the matrix that defines the overall
anisotropic displacement model if one was refined for this
structure.
refine.correlation_coeff_Fo_to_Fc
The correlation coefficient between the observed and
calculated structure factors for reflections included in
the refinement.
The correlation coefficient is scale-independent and gives
an idea of the quality of the refined model.
sum~i~(Fo~i~ Fc~i~ - <Fo><Fc>)
R~corr~ = ------------------------------------------------------------
SQRT{sum~i~(Fo~i~)^2^-<Fo>^2^} SQRT{sum~i~(Fc~i~)^2^-<Fc>^2^}
Fo = observed structure factors
Fc = calculated structure factors
<> denotes average value
summation is over reflections included in the refinement
refine.correlation_coeff_Fo_to_Fc_free
The correlation coefficient between the observed and
calculated structure factors for reflections not included
in the refinement (free reflections).
The correlation coefficient is scale-independent and gives
an idea of the quality of the refined model.
sum~i~(Fo~i~ Fc~i~ - <Fo><Fc>)
R~corr~ = ------------------------------------------------------------
SQRT{sum~i~(Fo~i~)^2^-<Fo>^2^} SQRT{sum~i~(Fc~i~)^2^-<Fc>^2^}
Fo = observed structure factors
Fc = calculated structure factors
<> denotes average value
summation is over reflections not included
in the refinement (free reflections)
refine.details
Description of special aspects of the refinement process.
refine.diff_density_max
The maximum value of the electron density in the final difference
Fourier map.
refine.diff_density_max_esd
The standard uncertainty (estimated standard deviation)
of attribute diff_density_max in category refine.
refine.diff_density_min
The minimum value of the electron density in the final difference
Fourier map.
refine.diff_density_min_esd
The standard uncertainty (estimated standard deviation)
of attribute diff_density_min in category refine.
refine.diff_density_rms
The root-mean-square-deviation of the electron density in the
final difference Fourier map. This value is measured with respect
to the arithmetic mean density and is derived from summations
over each grid point in the asymmetric unit of the cell. This
quantity is useful for assessing the significance of the values
of _refine.diff_density_min and _refine.diff_density_max, and
also for defining suitable contour levels.
refine.diff_density_rms_esd
The standard uncertainty (estimated standard deviation)
of attribute diff_density_rms in category refine.
refine.ls_R_Fsqd_factor_obs
Residual factor R(Fsqd) for reflections that satisfy the
resolution limits established by attribute ls_d_res_high in category refine and
attribute ls_d_res_low in category refine and the observation limit established by
attribute observed_criterion in category reflns, calculated on the squares of the
observed and calculated structure-factor amplitudes.
sum|F~obs~^2^ - F~calc~^2^|
R(Fsqd) = ---------------------------
sum|F~obs~^2^|
F~obs~^2^ = squares of the observed structure-factor amplitudes
F~calc~^2^ = squares of the calculated structure-factor
amplitudes
sum is taken over the specified reflections
refine.ls_R_I_factor_obs
Residual factor R(I) for reflections that satisfy the
resolution limits established by attribute ls_d_res_high in category refine and
attribute ls_d_res_low in category refine and the observation limit established by
attribute observed_criterion in category reflns, calculated on the estimated
reflection intensities.
This is most often calculated in Rietveld refinements against
powder data, where it is referred to as R~B~ or R~Bragg~.
sum|I~obs~ - I~calc~|
R(I) = ---------------------
sum|I~obs~|
I~obs~ = the net observed intensities
I~calc~ = the net calculated intensities
sum is taken over the specified reflections
refine.ls_R_factor_R_free
Residual factor R for reflections that satisfy the resolution
limits established by attribute ls_d_res_high in category refine and
attribute ls_d_res_low in category refine and the observation limit established by
attribute observed_criterion in category reflns, and that were used as the test
reflections (i.e. were excluded from the refinement) when the
refinement included the calculation of a 'free' R factor.
Details of how reflections were assigned to the working and
test sets are given in attribute R_free_details.
in category reflns
sum|F~obs~ - F~calc~|
R = ---------------------
sum|F~obs~|
F~obs~ = the observed structure-factor amplitudes
F~calc~ = the calculated structure-factor amplitudes
sum is taken over the specified reflections
refine.ls_R_factor_R_free_error
The estimated error in attribute ls_R_factor_R_free.
in category refine The method used to estimate the error is described in the
item attribute ls_R_factor_R_free_error_details in category refine.
refine.ls_R_factor_R_free_error_details
Special aspects of the method used to estimated the error in
attribute ls_R_factor_R_free in category refine.
refine.ls_R_factor_R_work
Residual factor R for reflections that satisfy the resolution
limits established by attribute ls_d_res_high in category refine and
attribute ls_d_res_low in category refine and the observation limit established by
attribute observed_criterion in category reflns, and that were used as the working
reflections (i.e. were included in the refinement) when the
refinement included the calculation of a 'free' R factor.
Details of how reflections were assigned to the working and
test sets are given in attribute R_free_details.
in category reflns
attribute ls_R_factor_obs in category refine should not be confused with
attribute ls_R_factor_R_work in category refine; the former reports the results of a
refinement in which all observed reflections were used, the
latter a refinement in which a subset of the observed
reflections were excluded from refinement for the calculation
of a 'free' R factor. However, it would be meaningful to quote
both values if a 'free' R factor were calculated for most of
the refinement, but all of the observed reflections were used
in the final rounds of refinement; such a protocol should be
explained in attribute details.
in category refine
sum|F~obs~ - F~calc~|
R = ---------------------
sum|F~obs~|
F~obs~ = the observed structure-factor amplitudes
F~calc~ = the calculated structure-factor amplitudes
sum is taken over the specified reflections
refine.ls_R_factor_all
Residual factor R for all reflections that satisfy the resolution
limits established by attribute ls_d_res_high in category refine and
attribute ls_d_res_low.
in category refine
sum|F~obs~ - F~calc~|
R = ---------------------
sum|F~obs~|
F~obs~ = the observed structure-factor amplitudes
F~calc~ = the calculated structure-factor amplitudes
sum is taken over the specified reflections
refine.ls_R_factor_gt
Residual factor for the reflections (with number given by
attribute number_gt) in category reflns judged significantly intense (i.e. satisfying
the threshold specified by attribute threshold_expression)
in category reflns and included in the refinement. The reflections also satisfy
the resolution limits established by attribute ls_d_res_high in category refine and
attribute ls_d_res_low in category refine. This is the conventional R
factor. See also attribute ls_wR_factor_ in category refine definitions.
sum | F(obs) - F(calc) |
R = ------------------------
sum | F(obs) |
F(obs) = the observed structure-factor amplitudes
F(calc) = the calculated structure-factor amplitudes
and the sum is taken over the specified reflections
refine.ls_R_factor_obs
Residual factor R for reflections that satisfy the resolution
limits established by attribute ls_d_res_high in category refine and
attribute ls_d_res_low in category refine and the observation limit established by
attribute observed_criterion.
in category reflns
attribute ls_R_factor_obs in category refine should not be confused with
attribute ls_R_factor_R_work in category refine; the former reports the results of a
refinement in which all observed reflections were used, the
latter a refinement in which a subset of the observed
reflections were excluded from refinement for the calculation
of a 'free' R factor. However, it would be meaningful to quote
both values if a 'free' R factor were calculated for most of
the refinement, but all of the observed reflections were used
in the final rounds of refinement; such a protocol should be
explained in attribute details.
in category refine
sum|F~obs~ - F~calc~|
R = ---------------------
sum|F~obs~|
F~obs~ = the observed structure-factor amplitudes
F~calc~ = the calculated structure-factor amplitudes
sum is taken over the specified reflections
refine.ls_abs_structure_Flack
The measure of absolute structure (enantiomorph or polarity) as
defined by Flack (1983).
For centrosymmetric structures, the only permitted value, if the
data name is present, is 'inapplicable', represented by '.' .
For noncentrosymmetric structures the value must lie in the
99.97% Gaussian confidence interval -3u =< x =< 1 + 3u and a
standard uncertainty (estimated standard deviation) u must
be supplied. The item range of [0.0:1.0] is correctly
interpreted as meaning (0.0 - 3u) =< x =< (1.0 + 3u).
Ref: Flack, H. D. (1983). Acta Cryst. A39, 876-881.
refine.ls_abs_structure_Flack_esd
The standard uncertainty (estimated standard deviation)
of attribute ls_abs_structure_Flack in category refine.
refine.ls_abs_structure_Rogers
The measure of absolute structure (enantiomorph or polarity) as
defined by Rogers.
The value must lie in the 99.97% Gaussian confidence interval
-1 -3u =< \h =< 1 + 3u and a standard uncertainty (estimated
standard deviation) u must be supplied. The item range of
[-1.0, 1.0] is correctly interpreted as meaning
(-1.0 - 3u) =< \h =< (1.0 + 3u).
Ref: Rogers, D. (1981). Acta Cryst. A37, 734-741.
refine.ls_abs_structure_Rogers_esd
The standard uncertainty (estimated standard deviation)
of attribute ls_abs_structure_Rogers in category refine.
refine.ls_abs_structure_details
The nature of the absolute structure and how it was determined.
For example, this may describe the Friedel pairs used.
refine.ls_d_res_high
The smallest value for the interplanar spacings for the
reflection data used in the refinement in angstroms. This is
called the highest resolution.
refine.ls_d_res_low
The largest value for the interplanar spacings for
the reflection data used in the refinement in angstroms.
This is called the lowest resolution.
refine.ls_extinction_coef
The extinction coefficient used to calculate the correction
factor applied to the structure-factor data. The nature of the
extinction coefficient is given in the definitions of
attribute ls_extinction_expression in category refine and
attribute ls_extinction_method.
in category refine
For the 'Zachariasen' method it is the r* value; for the
'Becker-Coppens type 1 isotropic' method it is the 'g' value,
and for 'Becker-Coppens type 2 isotropic' corrections it is
the 'rho' value. Note that the magnitude of these values is
usually of the order of 10000.
Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30,
129-47, 148-153.
Zachariasen, W. H. (1967). Acta Cryst. 23, 558-564.
Larson, A. C. (1967). Acta Cryst. 23, 664-665.
Zachariasen coefficient r* = 0.347 E04
3472
refine.ls_extinction_coef_esd
The standard uncertainty (estimated standard deviation)
of attribute ls_extinction_coef in category refine.
refine.ls_extinction_expression
A description of or reference to the extinction-correction
equation used to apply the data item
attribute ls_extinction_coef in category refine. This information must be sufficient
to reproduce the extinction-correction factors applied to the
structure factors.
Larson, A. C. (1970). "Crystallographic Computing", edited by
F. R. Ahmed. Eq. (22), p.292. Copenhagen: Munksgaard.
refine.ls_extinction_method
A description of the extinction-correction method applied.
This description should
include information about the correction method, either
'Becker-Coppens' or 'Zachariasen'. The latter is sometimes
referred to as the 'Larson' method even though it employs
Zachariasen's formula.
The Becker-Coppens procedure is referred to as 'type 1' when
correcting secondary extinction dominated by the mosaic spread;
as 'type 2' when secondary extinction is dominated by particle
size and includes a primary extinction component; and as 'mixed'
when there is a mixture of types 1 and 2.
For the Becker-Coppens method, it is also necessary to set the
mosaic distribution as either 'Gaussian' or 'Lorentzian' and the
nature of the extinction as 'isotropic' or 'anisotropic'. Note
that if either the 'mixed' or 'anisotropic' corrections are
applied, the multiple coefficients cannot be contained in
*_extinction_coef and must be listed in attribute details.
in category refine
Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30,
129-147, 148-153.
Zachariasen, W. H. (1967). Acta Cryst. 23, 558- 564.
Larson, A. C. (1967). Acta Cryst. 23, 664-665.
B-C type 2 Gaussian isotropic
refine.ls_goodness_of_fit_all
The least-squares goodness-of-fit parameter S for all data
after the final cycle of refinement. Ideally, account should be
taken of parameters restrained in the least-squares refinement.
See also the definition of attribute ls_restrained_S_all.
in category refine
( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^
S = ( ---------------------------- )
( N~ref~ - N~param~ )
Y~obs~ = the observed coefficients
(see attribute ls_structure_factor_coef)
in category refine Y~calc~ = the calculated coefficients
(see attribute ls_structure_factor_coef)
in category refine w = the least-squares reflection weight
[1/(e.s.d. squared)]
N~ref~ = the number of reflections used in the refinement
N~param~ = the number of refined parameters
sum is taken over the specified reflections
refine.ls_goodness_of_fit_all_esd
The standard uncertainty (estimated standard deviation)
of attribute ls_goodness_of_fit_all in category refine.
refine.ls_goodness_of_fit_gt
The least-squares goodness-of-fit parameter S for
significantly intense reflections (see
attribute threshold_expression) in category reflns after the final cycle of
refinement. Ideally, account should be taken of parameters
restrained in the least-squares refinement. See also
attribute ls_restrained_S_ in category refine definitions.
{ sum { w [ Y(obs) - Y(calc) ]^2^ } }^1/2^
S = { ----------------------------------- }
{ Nref - Nparam }
Y(obs) = the observed coefficients
(see _refine_ls_structure_factor_coef)
Y(calc) = the calculated coefficients
(see _refine_ls_structure_factor_coef)
w = the least-squares reflection weight
[1/(u^2^)]
u = standard uncertainty
Nref = the number of reflections used in the refinement
Nparam = the number of refined parameters
and the sum is taken over the specified reflections
refine.ls_goodness_of_fit_obs
The least-squares goodness-of-fit parameter S for reflection data
classified as 'observed' (see attribute observed_criterion) in category reflns after
the final cycle of refinement. Ideally, account should be taken
of parameters restrained in the least-squares refinement.
See also the definition of attribute ls_restrained_S_obs.
in category refine
( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^
S = ( ---------------------------- )
( N~ref~ - N~param~ )
Y~obs~ = the observed coefficients
(see attribute ls_structure_factor_coef)
in category refine Y~calc~ = the calculated coefficients
(see attribute ls_structure_factor_coef)
in category refine w = the least-squares reflection weight
[1/(e.s.d. squared)]
N~ref~ = the number of reflections used in the refinement
N~param~ = the number of refined parameters
sum is taken over the specified reflections
refine.ls_goodness_of_fit_obs_esd
The standard uncertainty (estimated standard deviation)
of attribute ls_goodness_of_fit_obs in category refine.
refine.ls_goodness_of_fit_ref
The least-squares goodness-of-fit parameter S for all
reflections included in the refinement after the final cycle
of refinement. Ideally, account should be taken of parameters
restrained in the least-squares refinement. See also
_refine_ls_restrained_S_ definitions.
{ sum | w | Y(obs) - Y(calc) |^2^ | }^1/2^
S = { ----------------------------------- }
{ Nref - Nparam }
Y(obs) = the observed coefficients
(see _refine_ls_structure_factor_coef)
Y(calc) = the calculated coefficients
(see _refine_ls_structure_factor_coef)
w = the least-squares reflection weight
[1/(u^2^)]
u = standard uncertainty
Nref = the number of reflections used in the refinement
Nparam = the number of refined parameters
and the sum is taken over the specified reflections
refall
refxyz
refU
noref
constr
mixed
undef
Treatment of hydrogen atoms in the least-squares refinement.
full
fullcycle
atomblock
userblock
diagonal
sparse
Type of matrix used to accumulate the least-squares derivatives.
refine.ls_number_constraints
The number of constrained (non-refined or dependent) parameters
in the least-squares process. These may be due to symmetry or any
other constraint process (e.g. rigid-body refinement). See also
_atom_site.constraints and _atom_site.refinement_flags. A general
description of constraints may appear in attribute details in category refine.
refine.ls_number_parameters
The number of parameters refined in the least-squares process.
If possible, this number should include some contribution from
the restrained parameters. The restrained parameters are
distinct from the constrained parameters (where one or more
parameters are linearly dependent on the refined value of
another). Least-squares restraints often depend on geometry or
energy considerations and this makes their direct contribution
to this number, and to the goodness-of-fit calculation,
difficult to assess.
refine.ls_number_reflns_R_free
The number of reflections that satisfy the resolution limits
established by _refine.ls_d_res_high and _refine.ls_d_res_low
and the observation limit established by
attribute observed_criterion in category reflns, and that were used as the test
reflections (i.e. were excluded from the refinement) when the
refinement included the calculation of a 'free' R factor.
Details of how reflections were assigned to the working and
test sets are given in attribute R_free_details in category reflns.
refine.ls_number_reflns_R_work
The number of reflections that satisfy the resolution limits
established by _refine.ls_d_res_high and _refine.ls_d_res_low
and the observation limit established by
attribute observed_criterion in category reflns, and that were used as the working
reflections (i.e. were included in the refinement) when the
refinement included the calculation of a 'free' R factor.
Details of how reflections were assigned to the working and
test sets are given in attribute R_free_details in category reflns.
refine.ls_number_reflns_all
The number of reflections that satisfy the resolution limits
established by _refine.ls_d_res_high and _refine.ls_d_res_low.
refine.ls_number_reflns_obs
The number of reflections that satisfy the resolution limits
established by _refine.ls_d_res_high and _refine.ls_d_res_low
and the observation limit established by
attribute observed_criterion in category reflns.
refine.ls_number_restraints
The number of restrained parameters. These are parameters which
are not directly dependent on another refined parameter.
Restrained parameters often involve geometry or energy
dependencies.
See also _atom_site.constraints and _atom_site.refinement_flags.
A general description of refinement constraints may appear in
attribute details in category refine.
refine.ls_percent_reflns_R_free
The number of reflections that satisfy the resolution limits
established by _refine.ls_d_res_high and _refine.ls_d_res_low
and the observation limit established by
attribute observed_criterion in category reflns, and that were used as the test
reflections (i.e. were excluded from the refinement) when the
refinement included the calculation of a 'free' R factor,
expressed as a percentage of the number of geometrically
observable reflections that satisfy the resolution limits.
refine.ls_percent_reflns_obs
The number of reflections that satisfy the resolution limits
established by _refine.ls_d_res_high and _refine.ls_d_res_low
and the observation limit established by
attribute observed_criterion in category reflns, expressed as a percentage of the
number of geometrically observable reflections that satisfy
the resolution limits.
refine.ls_redundancy_reflns_all
The ratio of the total number of observations of the
reflections that satisfy the resolution limits established by
_refine.ls_d_res_high and _refine.ls_d_res_low to the number
of crystallographically unique reflections that satisfy the
same limits.
refine.ls_redundancy_reflns_obs
The ratio of the total number of observations of the
reflections that satisfy the resolution limits established by
_refine.ls_d_res_high and _refine.ls_d_res_low and the
observation limit established by attribute observed_criterion in category reflns to
the number of crystallographically unique reflections that
satisfy the same limits.
refine.ls_restrained_S_all
The least-squares goodness-of-fit parameter S' for all
reflections after the final cycle of least-squares refinement.
This parameter explicitly includes the restraints applied
in the least-squares process. See also the definition of
attribute ls_goodness_of_fit_all.
in category refine
( sum |w |Y~obs~ - Y~calc~|^2^| )^1/2^
( + sum~r~|w~r~ |P~calc~ - P~targ~|^2^| )
S' = ( ------------------------------------- )
( N~ref~ + N~restr~ - N~param~ )
Y~obs~ = the observed coefficients
(see attribute ls_structure_factor_coef)
in category refine Y~calc~ = the calculated coefficients
(see attribute ls_structure_factor_coef)
in category refine w = the least-squares reflection weight
[1/(e.s.d. squared)]
P~calc~ = the calculated restraint values
P~targ~ = the target restraint values
w~r~ = the restraint weight
N~ref~ = the number of reflections used in the refinement
(see attribute ls_number_reflns_obs)
in category refine N~restr~ = the number of restraints
(see attribute ls_number_restraints)
in category refine N~param~ = the number of refined parameters
(see attribute ls_number_parameters)
in category refine
sum is taken over the specified reflections
sumr is taken over the restraints
refine.ls_restrained_S_obs
The least-squares goodness-of-fit parameter S' for reflection
data classified as observed (see attribute observed_criterion)
in category reflns after the final cycle of least-squares refinement. This
parameter explicitly includes the restraints applied in
the least-squares process. See also the definition of
attribute ls_goodness_of_fit_obs.
in category refine
( sum |w |Y~obs~ - Y~calc~|^2^| )^1/2^
( + sum~r~|w~r~ |P~calc~ - P~targ~|^2^| )
S' = ( ------------------------------------- )
( N~ref~ + N~restr~ - N~param~ )
Y~obs~ = the observed coefficients
(see attribute ls_structure_factor_coef)
in category refine Y~calc~ = the calculated coefficients
(see attribute ls_structure_factor_coef)
in category refine w = the least-squares reflection weight
[1/(e.s.d. squared)]
P~calc~ = the calculated restraint values
P~targ~ = the target restraint values
w~r~ = the restraint weight
N~ref~ = the number of reflections used in the refinement
(see attribute ls_number_reflns_obs)
in category refine N~restr~ = the number of restraints
(see attribute ls_number_restraints)
in category refine N~param~ = the number of refined parameters
(see attribute ls_number_parameters)
in category refine
sum is taken over the specified reflections
sumr is taken over the restraints
refine.ls_shift_over_esd_max
The largest ratio of the final least-squares parameter shift
to the final standard uncertainty (estimated standard
deviation).
refine.ls_shift_over_esd_mean
The average ratio of the final least-squares parameter shift
to the final standard uncertainty (estimated standard
deviation).
refine.ls_shift_over_su_max
The largest ratio of the final least-squares parameter
shift to the final standard uncertainty.
refine.ls_shift_over_su_max_lt
An upper limit for the largest ratio of the final
least-squares parameter shift to the final
standard uncertainty. This item is used when the largest
value of the shift divided by the final standard uncertainty
is too small to measure.
refine.ls_shift_over_su_mean
The average ratio of the final least-squares parameter
shift to the final standard uncertainty.
refine.ls_shift_over_su_mean_lt
An upper limit for the average ratio of the final
least-squares parameter shift to the
final standard uncertainty. This
item is used when the average value of the shift divided by
the final standard uncertainty is too small to measure.
F
Fsqd
Inet
Structure-factor coefficient |F|, F^2^ or I used in the least-
squares refinement process.
refine.ls_wR_factor_R_free
Weighted residual factor wR for reflections that satisfy the
resolution limits established by attribute ls_d_res_high in category refine and
attribute ls_d_res_low in category refine and the observation limit established by
attribute observed_criterion in category reflns, and that were used as the test
reflections (i.e. were excluded from the refinement) when the
refinement included the calculation of a 'free' R factor.
Details of how reflections were assigned to the working and
test sets are given in attribute R_free_details.
in category reflns
( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^
wR = ( ---------------------------- )
( sum|w Y~obs~^2^| )
Y~obs~ = the observed amplitude specified by
attribute ls_structure_factor_coef
in category refine Y~calc~ = the calculated amplitude specified by
attribute ls_structure_factor_coef
in category refine w = the least-squares weight
sum is taken over the specified reflections
refine.ls_wR_factor_R_work
Weighted residual factor wR for reflections that satisfy the
resolution limits established by attribute ls_d_res_high in category refine and
attribute ls_d_res_low in category refine and the observation limit established by
attribute observed_criterion in category reflns, and that were used as the working
reflections (i.e. were included in the refinement) when the
refinement included the calculation of a 'free' R factor.
Details of how reflections were assigned to the working and
test sets are given in attribute R_free_details.
in category reflns
( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^
wR = ( ---------------------------- )
( sum|w Y~obs~^2^| )
Y~obs~ = the observed amplitude specified by
attribute ls_structure_factor_coef
in category refine Y~calc~ = the calculated amplitude specified by
attribute ls_structure_factor_coef
in category refine w = the least-squares weight
sum is taken over the specified reflections
refine.ls_wR_factor_all
Weighted residual factor wR for all reflections that satisfy the
resolution limits established by attribute ls_d_res_high in category refine and
attribute ls_d_res_low.
in category refine
( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^
wR = ( ---------------------------- )
( sum|w Y~obs~^2^| )
Y~obs~ = the observed amplitude specified by
attribute ls_structure_factor_coef
in category refine Y~calc~ = the calculated amplitude specified by
attribute ls_structure_factor_coef
in category refine w = the least-squares weight
sum is taken over the specified reflections
refine.ls_wR_factor_obs
Weighted residual factor wR for reflections that satisfy the
resolution limits established by attribute ls_d_res_high in category refine and
attribute ls_d_res_low in category refine and the observation limit established by
attribute observed_criterion.
in category reflns
( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^
wR = ( ---------------------------- )
( sum|w Y~obs~^2^| )
Y~obs~ = the observed amplitude specified by
attribute ls_structure_factor_coef
in category refine Y~calc~ = the calculated amplitude specified by
attribute ls_structure_factor_coef
in category refine w = the least-squares weight
sum is taken over the specified reflections
refine.ls_weighting_details
A description of special aspects of the weighting scheme used
in least-squares refinement. Used to describe the weighting
when the value of attribute ls_weighting_scheme in category refine is specified
as 'calc'.
Sigdel model of Konnert-Hendrickson:
Sigdel =
Afsig + Bfsig*(sin(theta)/lambda-1/6)
Afsig = 22.0, Bfsig = 150.0
at the beginning of refinement.
Afsig = 16.0, Bfsig = 60.0
at the end of refinement.
sigma
unit
calc
The weighting scheme applied in the least-squares process. The
standard code may be followed by a description of the weight
(but see attribute ls_weighting_details in category refine for a preferred approach).
refine.occupancy_max
The maximum value for occupancy found in the coordinate set.
refine.occupancy_min
The minimum value for occupancy found in the coordinate set.
refine.overall_FOM_free_R_set
Average figure of merit of phases of reflections not included
in the refinement.
This value is derived from the likelihood function.
FOM = I_1(X)/I_0(X)
I_0, I_1 = zero- and first-order modified Bessel functions
of the first kind
X = sigma_A |E_o| |E_c|/SIGMA
E_o, E_c = normalized observed and calculated structure
factors
sigma_A = <cos 2 pi s delta_x> SQRT(Sigma_P/Sigma_N)
estimated using maximum likelihood
Sigma_P = sum_{atoms in model} f^2
Sigma_N = sum_{atoms in crystal} f^2
f = form factor of atoms
delta_x = expected error
SIGMA = (sigma_{E;exp})^2 + epsilon [1-(sigma_A)^2]
sigma_{E;exp} = uncertainties of normalized observed
structure factors
epsilon = multiplicity of the diffracting plane
Ref: Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997).
Acta Cryst. D53, 240-255.
refine.overall_FOM_work_R_set
Average figure of merit of phases of reflections included in
the refinement.
This value is derived from the likelihood function
FOM = I_1(X)/I_0(X)
I_0, I_1 = zero- and first-order modified Bessel functions
of the first kind
X = sigma_A |E_o| |E_c|/SIGMA
E_o, E_c = normalized observed and calculated structure
factors
sigma_A = <cos 2 pi s delta_x> SQRT(Sigma_P/Sigma_N)
estimated using maximum likelihood
Sigma_P = sum_{atoms in model} f^2
Sigma_N = sum_{atoms in crystal} f^2
f = form factor of atoms
delta_x = expected error
SIGMA = (sigma_{E;exp})^2 + epsilon [1-(sigma_A)^2]
sigma_{E;exp} = uncertainties of normalized observed
structure factors
epsilon = multiplicity of diffracting plane
Ref: Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997).
Acta Cryst. D53, 240-255.
refine.overall_SU_B
The overall standard uncertainty (estimated standard deviation)
of the displacement parameters based on a maximum-likelihood
residual.
The overall standard uncertainty (sigma~B~)^2 gives an idea
of the uncertainty in the B values of averagely defined
atoms (atoms with B values equal to the average B value).
N_a
(sigma~B~)^2 = 8 ----------------------------------------------
sum~i~ {[1/Sigma - (E_o)^2 (1-m^2)](SUM_AS)s^4}
SUM_AS = (sigma_A)^2/Sigma^2
N_a = number of atoms
Sigma = (sigma_{E;exp})^2 + epsilon [1-(sigma_A)^2]
E_o = normalized structure factors
sigma_{E;exp} = experimental uncertainties of normalized
structure factors
sigma_A = <cos 2 pi s delta_x> SQRT(Sigma_P/Sigma_N)
estimated using maximum likelihood
Sigma_P = sum_{atoms in model} f^2
Sigma_N = sum_{atoms in crystal} f^2
f = form factor of atoms
delta_x = expected error
m = figure of merit of phases of reflections
included in the summation
s = reciprocal-space vector
epsilon = multiplicity of diffracting plane
summation is over all reflections included in refinement
Ref: (sigma_A estimation) "Refinement of macromolecular
structures by the maximum-likelihood method",
Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997).
Acta Cryst. D53, 240-255.
(SU ML estimation) Murshudov, G. N. & Dodson,
E. J. (1997). Simplified error estimation a la
Cruickshank in macromolecular crystallography.
CCP4 Newsletter on Protein Crystallography, No. 33,
January 1997, pp. 31-39.
http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html
refine.overall_SU_ML
The overall standard uncertainty (estimated standard deviation)
of the positional parameters based on a maximum likelihood
residual.
The overall standard uncertainty (sigma~X~)^2 gives an
idea of the uncertainty in the position of averagely
defined atoms (atoms with B values equal to average B value)
3 N_a
(sigma~X~)^2 = -----------------------------------------------------
8 pi^2 sum~i~ {[1/Sigma - (E_o)^2 (1-m^2)](SUM_AS)s^2}
SUM_AS = (sigma_A)^2/Sigma^2)
N_a = number of atoms
Sigma = (sigma_{E;exp})^2 + epsilon [1-{sigma_A)^2]
E_o = normalized structure factors
sigma_{E;exp} = experimental uncertainties of normalized
structure factors
sigma_A = <cos 2 pi s delta_x> SQRT(Sigma_P/Sigma_N)
estimated using maximum likelihood
Sigma_P = sum_{atoms in model} f^2
Sigma_N = sum_{atoms in crystal} f^2
f = form factor of atoms
delta_x = expected error
m = figure of merit of phases of reflections
included in the summation
s = reciprocal-space vector
epsilon = multiplicity of the diffracting plane
summation is over all reflections included in refinement
Ref: (sigma_A estimation) "Refinement of macromolecular
structures by the maximum-likelihood method",
Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997).
Acta Cryst. D53, 240-255.
(SU ML estimation) Murshudov, G. N. & Dodson,
E. J. (1997). Simplified error estimation a la
Cruickshank in macromolecular crystallography.
CCP4 Newsletter on Protein Crystallography, No. 33,
January 1997, pp. 31-39.
http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html
refine.overall_SU_R_Cruickshank_DPI
The overall standard uncertainty (estimated standard deviation)
of the displacement parameters based on the crystallographic
R value, expressed in a formalism known as the dispersion
precision indicator (DPI).
The overall standard uncertainty (sigma~B~) gives an idea
of the uncertainty in the B values of averagely defined
atoms (atoms with B values equal to the average B value).
N_a
(sigma_B)^2 = 0.65 --------- (R_value)^2 (D_min)^2 C^(-2/3)
(N_o-N_p)
N_a = number of atoms
N_o = number of reflections included in refinement
N_p = number of refined parameters
R_value = conventional crystallographic R value
D_min = maximum resolution
C = completeness of data
Ref: Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601.
Murshudov, G. N. & Dodson,
E. J. (1997). Simplified error estimation a la
Cruickshank in macromolecular crystallography.
CCP4 Newsletter on Protein Crystallography, No. 33,
January 1997, pp. 31-39.
http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html
refine.overall_SU_R_free
The overall standard uncertainty (estimated standard deviation)
of the displacement parameters based on the free R value.
The overall standard uncertainty gives an idea of the
uncertainty in the B values of averagely defined atoms
(atoms with B values equal to the average B value).
N_a
(sigma_B)^2 = 0.65 ----- (R_free)^2 (D_min)^2 C^(-2/3)
N_o
N_a = number of atoms
N_o = number of reflections included in refinement
R_free = conventional free crystallographic R value calculated
using reflections not included in refinement
D_min = maximum resolution
C = completeness of data
Ref: Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601.
Murshudov, G. N. & Dodson,
E. J. (1997). Simplified error estimation a la
Cruickshank in macromolecular crystallography.
CCP4 Newsletter on Protein Crystallography, No. 33,
January 1997, pp. 31-39.
http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html
refine.pdbx_R_Free_selection_details
Details of the manner in which the cross validation
reflections were selected.
Random selection
refine.pdbx_data_cutoff_high_absF
Value of F at "high end" of data cutoff.
17600
refine.pdbx_data_cutoff_high_rms_absF
Value of RMS |F| used as high data cutoff.
205.1
refine.pdbx_data_cutoff_low_absF
Value of F at "low end" of data cutoff.
0.30
refine.pdbx_density_correlation
The density correlation coefficient is calculated from atomic
densities of (2Fobs-Fcalc) map - "Robs" and the model
map (Fcalc) - "Rcalc" :
D_corr = <Robs><Rcalc>/sqrt(<Robs**2><Rcalc**2>)
where <Robs> is the mean of "observed" densities of all atoms
<Rcalc> is the mean of "calculated" densities of
all atoms.
The value of density for some atom from map R(x) is:
sum_i ( R(xi) * Ratom(xi - xa) )
Dens = ----------------------------------
sum_i ( Ratom(xi - xa) )
where Ratom(x) is atomic electron density for the x-th grid point.
xa - vector of the centre of atom.
xi - vector of the i-th point of grid.
Sum is taken over all grid points which have distance
from the center of the atom less than the Radius_limit.
For all atoms Radius_limit = 2.5 A.
Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205
refine.pdbx_isotropic_thermal_model
Whether the structure was refined with indvidual
isotropic, anisotropic or overall temperature factor.
Isotropic
Overall
refine.pdbx_ls_cross_valid_method
Whether the cross validataion method was used through
out or only at the end.
FREE R-VALUE
refine.pdbx_ls_sigma_F
Data cutoff (SIGMA(F))
refine.pdbx_ls_sigma_Fsqd
Data cutoff (SIGMA(F^2))
refine.pdbx_ls_sigma_I
Data cutoff (SIGMA(I))
refine.pdbx_method_to_determine_struct
Method(s) used to determine the structure.
AB INITIO PHASING
Direct Methods
DM
Iterative Single wavelength Anomalous Scattering
ISAS
Iterative Single Isomorphous Replacement
ISIR
Iterative Single Isomorphous Replacement with Anomalous Scattering
ISIRAS
Multi wavelength Anomalous Diffraction
MAD
Multiple Isomorphous Replacement
MIR
Multiple Isomorphous Replacement with Anomalous Scattering
MIRAS
Molecular Replacement
MR
Single Isomorphous Replacement
SIR
Single Isomorphous Replacement with Anomalous Scattering
SIRAS
refine.pdbx_overall_ESU_R
Overall estimated standard uncertainties of positional
parameters based on R value.
refine.pdbx_overall_ESU_R_Free
Overall estimated standard uncertainties of positional
parameters based on R value.
refine.pdbx_overall_SU_R_Blow_DPI
The overall standard uncertainty (estimated standard deviation)
of the displacement parameters based on the crystallographic
R value, expressed in a formalism known as the dispersion
precision indicator (DPI).
Ref: Blow, D (2002) Acta Cryst. D58, 792-797
refine.pdbx_overall_SU_R_free_Blow_DPI
The overall standard uncertainty (estimated standard deviation)
of the displacement parameters based on the crystallographic
R-free value, expressed in a formalism known as the dispersion
precision indicator (DPI).
Ref: Blow, D (2002) Acta Cryst. D58, 792-797
refine.pdbx_overall_SU_R_free_Cruickshank_DPI
The overall standard uncertainty (estimated standard deviation)
of the displacement parameters based on the crystallographic
R-free value, expressed in a formalism known as the dispersion
precision indicator (DPI).
Ref: Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601.
refine.pdbx_overall_phase_error
The overall phase error for all reflections after refinement using
the current refinement target.
0.30
refine.pdbx_pd_Fsqrd_R_factor
Residual factor R for reflections that satisfy the resolution
limits established by attribute ls_d_res_high in category refine and
attribute ls_d_res_low in category refine and the observation limit established by
attribute observed_criterion.
in category reflns sum|F~obs~**2 - F~calc~**2|
R = ---------------------
sum|F~obs~**2|
F~obs~ = the observed structure-factor amplitudes
F~calc~ = the calculated structure-factor amplitudes
sum is taken over the specified reflections
refine.pdbx_pd_Marquardt_correlation_coeff
The correlation coefficient between the observed and
calculated structure factors for reflections included in
the refinement. This correlation factor is found in the
fitting using the Levenberg-Marquardt algorithm to search
for the minimum value of chisquare. Almost all computer
codes for Rietveld refinement employ the Gauss-Newton algorithm
to find parameters which minimize the weighted sum of squares
of the residuals.
A description of the equations is given on
http://www.water.hut.fi/~tkarvone/fr_org_s.htm
refine.pdbx_pd_ls_matrix_band_width
The least squares refinement "band matrix" approximation to the full matrix.
refine.pdbx_pd_meas_number_of_points
The total number of points in the measured
diffractogram.
refine.pdbx_pd_number_of_points
The total number of data points in the processed diffractogram.
refine.pdbx_pd_number_of_powder_patterns
The total number of powder patterns used.
refine.pdbx_pd_proc_ls_prof_R_factor
Rietveld/Profile fit R factors.
Note that the R factor computed for Rietveld refinements
using the extracted reflection intensity values (often
called the Rietveld or Bragg R factor, R~B~) is not properly
a profile R factor.
pdbx_pd_proc_ls_prof_R_factor, often called R~p~, is an
unweighted fitness metric for the agreement between the
observed and computed diffraction patterns
R~p~ = sum~i~ | I~obs~(i) - I~calc~(i) |
/ sum~i~ ( I~obs~(i) )
Note that in the above equations,
w(i) is the weight for the ith data point
I~obs~(i) is the observed intensity for the ith data
point, sometimes referred to as y~i~(obs) or
y~oi~.
I~calc~(i) is the computed intensity for the ith data
point with background and other corrections
applied to match the scale of the observed dataset,
sometimes referred to as y~i~(calc) or
y~ci~.
n is the total number of data points (see attribute pdbx_pd_number_of_points)
in category refine less the number of data points excluded from the refinement.
p is the total number of refined parameters.
refine.pdbx_pd_proc_ls_prof_wR_factor
Rietveld/Profile fit R factors.
Note that the R factor computed for Rietveld refinements
using the extracted reflection intensity values (often
called the Rietveld or Bragg R factor, R~B~) is not properly
a profile R factor.
pdbx_pd_proc_ls_prof_wR_factor often called R~wp~, is a
weighted fitness metric for the agreement between the
observed and computed diffraction patterns
R~wp~ = SQRT {
sum~i~ ( w(i) [ I~obs~(i) - I~calc~(i) ]^2^ )
/ sum~i~ ( w(i) [I~obs~(i)]^2^ ) }
Note that in the above equations,
w(i) is the weight for the ith data point
I~obs~(i) is the observed intensity for the ith data
point, sometimes referred to as y~i~(obs) or
y~oi~.
I~calc~(i) is the computed intensity for the ith data
point with background and other corrections
applied to match the scale of the observed dataset,
sometimes referred to as y~i~(calc) or
y~ci~.
n is the total number of data points (see attribute pdbx_pd_number_of_points)
in category refine less the number of data points excluded from the refinement.
p is the total number of refined parameters.
refine.pdbx_real_space_R
Real space R factor of electron density for all atoms.
The real space R factor is calculated by the equation
R_real = [Sum~i (|Dobs - Dcal|)]/[Sum~i (|Dobs + Dcal|)]
Where:
Dobs is the observed electron density,
Dcal is the calculated electron density,
summation is for all the grid points
Ref: Branden, C.I. & Jones, T.A. (1990). Nature, 343, 687-689
refine.pdbx_solvent_ion_probe_radii
CCP4 solvent ion proble radii
refine.pdbx_solvent_shrinkage_radii
CCP4 solvent shrinkage radii
refine.pdbx_solvent_vdw_probe_radii
CCP4 solvent proble van der Waals radii
refine.pdbx_starting_model
Starting model for refinement. Starting model for
molecular replacement should refer to a previous
structure or experiment.
BDL001
refine.pdbx_stereochem_target_val_spec_case
Special case of stereochemistry target values used
in SHELXL refinement.
refine.pdbx_stereochemistry_target_values
Stereochemistry target values used in refinement.
refine.solvent_model_details
Special aspects of the solvent model used during refinement.
refine.solvent_model_param_bsol
The value of the BSOL solvent-model parameter describing
the average isotropic displacement parameter of disordered
solvent atoms.
This is one of the two parameters (the other is
attribute solvent_model_param_ksol) in category refine in Tronrud's method of
modelling the contribution of bulk solvent to the
scattering. The standard scale factor is modified according
to the expression
k0 exp(-B0 * s^2^)[1-KSOL * exp(-BSOL * s^2^)]
where k0 and B0 are the scale factors for the protein.
Ref: Tronrud, D. E. (1997). Methods Enzymol. 277, 243-268.
refine.solvent_model_param_ksol
The value of the KSOL solvent-model parameter describing
the ratio of the electron density in the bulk solvent to the
electron density in the molecular solute.
This is one of the two parameters (the other is
attribute solvent_model_param_bsol) in category refine in Tronrud's method of
modelling the contribution of bulk solvent to the
scattering. The standard scale factor is modified according
to the expression
k0 exp(-B0 * s^2^)[1-KSOL * exp(-BSOL * s^2^)]
where k0 and B0 are the scale factors for the protein.
Ref: Tronrud, D. E. (1997). Methods Enzymol. 277, 243-268.
refine.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
refine.pdbx_refine_id
This data item uniquely identifies a refinement within an entry.
attribute pdbx_refine_id in category refine can be used to distinguish the results of
joint refinements.
refine_B_iso
Data items in the REFINE_B_ISO category record details about
the treatment of isotropic B factors (displacement parameters)
during refinement.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:refine_B_isoCategory>
<PDBx:refine_B_iso class="protein" pdbx_refine_id="X-ray">
<PDBx:treatment>isotropic</PDBx:treatment>
</PDBx:refine_B_iso>
<PDBx:refine_B_iso class="solvent" pdbx_refine_id="X-ray">
<PDBx:treatment>isotropic</PDBx:treatment>
</PDBx:refine_B_iso>
<PDBx:refine_B_iso class="inhibitor" pdbx_refine_id="X-ray">
<PDBx:treatment>isotropic</PDBx:treatment>
</PDBx:refine_B_iso>
</PDBx:refine_B_isoCategory>
0
1
0
1
0
1
1
1
refine_B_isoCategory
This property indicates that datablock
has a category element refine_B_iso.
refine_B_isoItem
Abstract Datatype property for refine_B_iso items.
reference_to_refine_B_iso
cross-reference to refine_B_iso
refine_B_iso.details
A description of special aspects of the isotropic B-factor
(displacement-parameter) refinement for the class of atoms
described in attribute class in category refine_B_iso.
The temperature factors of atoms in the side
chain of Arg 92 were held fixed due to
unstable behavior in refinement.
fixed
isotropic
anisotropic
The treatment of isotropic B-factor (displacement-parameter)
refinement for a class of atoms defined in attribute class in category refine_B_iso.
refine_B_iso.value
The value of the isotropic B factor (displacement parameter)
assigned to a class of atoms defined in attribute class.
in category refine_B_iso Meaningful only for atoms with fixed isotropic B factors.
refine_B_iso.class
A class of atoms treated similarly for isotropic B-factor
(displacement-parameter) refinement.
all
protein
solvent
sugar-phosphate backbone
refine_B_iso.pdbx_refine_id
This data item uniquely identifies a refinement within an entry.
attribute pdbx_refine_id in category refine_B_iso can be used to distinguish the results
of joint refinements.
refine_analyze
Data items in the REFINE_ANALYZE category record details
about the refined structure that are often used to analyze the
refinement and assess its quality. A given computer program
may or may not produce values corresponding to these data
names.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:refine_analyzeCategory>
<PDBx:refine_analyze entry_id="5HVP" pdbx_refine_id="X-ray">
<PDBx:Luzzati_coordinate_error_obs>0.056</PDBx:Luzzati_coordinate_error_obs>
<PDBx:Luzzati_d_res_low_obs>2.51</PDBx:Luzzati_d_res_low_obs>
</PDBx:refine_analyze>
</PDBx:refine_analyzeCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
refine_analyzeCategory
This property indicates that datablock
has a category element refine_analyze.
refine_analyzeItem
Abstract Datatype property for refine_analyze items.
reference_to_refine_analyze
cross-reference to refine_analyze
refine_analyze.Luzzati_coordinate_error_free
The estimated coordinate error obtained from the plot of
the R value versus sin(theta)/lambda for the reflections
treated as a test set during refinement.
Ref: Luzzati, V. (1952). Traitement statistique des erreurs
dans la determination des structures cristallines. Acta
Cryst. 5, 802-810.
refine_analyze.Luzzati_coordinate_error_obs
The estimated coordinate error obtained from the plot of
the R value versus sin(theta)/lambda for reflections classified
as observed.
Ref: Luzzati, V. (1952). Traitement statistique des erreurs
dans la determination des structures cristallines. Acta
Cryst. 5, 802-810.
refine_analyze.Luzzati_d_res_low_free
The value of the low-resolution cutoff used in constructing the
Luzzati plot for reflections treated as a test set during
refinement.
Ref: Luzzati, V. (1952). Traitement statistique des erreurs
dans la determination des structures cristallines. Acta
Cryst. 5, 802-810.
refine_analyze.Luzzati_d_res_low_obs
The value of the low-resolution cutoff used in
constructing the Luzzati plot for reflections classified as
observed.
Ref: Luzzati, V. (1952). Traitement statistique des erreurs
dans la determination des structures cristallines. Acta
Cryst. 5, 802-810.
refine_analyze.Luzzati_sigma_a_free
The value of sigma~a~ used in constructing the Luzzati plot for
the reflections treated as a test set during refinement.
Details of the estimation of sigma~a~ can be specified
in attribute Luzzati_sigma_a_free_details.
in category refine_analyze
Ref: Luzzati, V. (1952). Traitement statistique des erreurs
dans la determination des structures cristallines. Acta
Cryst. 5, 802-810.
refine_analyze.Luzzati_sigma_a_free_details
Details of the estimation of sigma~a~ for the reflections
treated as a test set during refinement.
Ref: Luzzati, V. (1952). Traitement statistique des erreurs
dans la determination des structures cristallines. Acta
Cryst. 5, 802-810.
refine_analyze.Luzzati_sigma_a_obs
The value of sigma~a~ used in constructing the Luzzati plot for
reflections classified as observed. Details of the
estimation of sigma~a~ can be specified in
attribute Luzzati_sigma_a_obs_details.
in category refine_analyze
Ref: Luzzati, V. (1952). Traitement statistique des erreurs
dans la determination des structures cristallines. Acta
Cryst. 5, 802-810.
refine_analyze.Luzzati_sigma_a_obs_details
Special aspects of the estimation of sigma~a~ for the
reflections classified as observed.
Ref: Luzzati, V. (1952). Traitement statistique des erreurs
dans la determination des structures cristallines. Acta
Cryst. 5, 802-810.
refine_analyze.RG_d_res_high
The value of the high-resolution cutoff in angstroms
used in the calculation of the Hamilton generalized
R factor (RG) stored in attribute RG_work in category refine_analyze and
attribute RG_free.
in category refine_analyze
Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510.
refine_analyze.RG_d_res_low
The value of the low-resolution cutoff in angstroms
used in the calculation of the Hamilton generalized
R factor (RG) stored in attribute RG_work in category refine_analyze and
attribute RG_free.
in category refine_analyze
Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510.
refine_analyze.RG_free
The Hamilton generalized R factor for all reflections that
satisfy the resolution limits established by
attribute RG_d_res_high in category refine_analyze and
attribute RG_d_res_low in category refine_analyze for the free R set of
reflections that were excluded from the refinement.
sum_i sum_j w_{i,j}(|Fobs|_i - G|Fcalc|_i)(|Fobs|_j - G|Fcalc|_j)
RG = Sqrt( ----------------------------------------------------------------- )
sum_i sum_j w_{i,j} |Fobs|_i |Fobs|_j
where
|Fobs| = the observed structure-factor amplitudes
|Fcalc| = the calculated structure-factor amplitudes
G = the scale factor which puts |Fcalc| on the
same scale as |Fobs|
w_{i,j} = the weight for the combination of the reflections
i and j.
sum_i and sum_j are taken over the specified reflections
When the covariance of the amplitudes of reflection i and
reflection j is zero (i.e. the reflections are independent)
w{i,i} can be redefined as w_i and the nested sums collapsed
into one sum.
sum_i w_i(|Fobs|_i - G|Fcalc|_i)^2
RG = Sqrt( ----------------------------------- )
sum_i w_i |Fobs|_i^2
Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510.
refine_analyze.RG_free_work_ratio
The observed ratio of RGfree to RGwork. The expected RG ratio
is the value that should be achievable at the end of a structure
refinement when only random uncorrelated errors exist in the data
and the model provided that the observations are properly
weighted. When compared with the observed RG ratio it may
indicate that a structure has not reached convergence or a
model has been over-refined with no corresponding improvement
in the model.
In an unrestrained refinement, the ratio of RGfree to RGwork with
only random uncorrelated errors at convergence depends only
on the number of reflections and the number of parameters
according to
sqrt[(f + m) / (f - m) ]
where f = the number of included structure amplitudes and
target distances, and
m = the number of parameters being refined.
In the restrained case, RGfree is calculated from a random
selection of residuals including both structure amplitudes
and restraints. When restraints are included in the refinement,
the RG ratio requires a term for the contribution to the
minimized residual at convergence, D~restr~, due to those
restraints:
D~restr~ = r - sum [w_i . (a_i)^t . (H)^-1 a_i]
where
r is the number of geometrical, displacement-parameter and
other restraints
H is the (m,m) normal matrix given by A^t.W.A
W is the (n,n) symmetric weight matrix of the included
observations
A is the least-squares design matrix of derivatives of
order (n,m)
a_i is the ith row of A
Then the expected RGratio becomes
sqrt [ (f + (m - r + D~restr~))/ (f - (m - r + D~restr~)) ]
There is no data name for the expected value of RGfree/RGwork yet.
Ref: Tickle, I. J., Laskowski, R. A. & Moss, D. S. (1998).
Acta Cryst. D54, 547-557.
refine_analyze.RG_work
The Hamilton generalized R factor for all reflections
that satisfy the resolution limits established by
attribute RG_d_res_high in category refine_analyze and
attribute RG_d_res_low in category refine_analyze and for those
reflections included in the working set when a free R set
of reflections is omitted from the refinement.
sum_i sum_j w_{i,j}(|Fobs|_i - G|Fcalc|_i)(|Fobs|_j - G|Fcalc|_j)
RG = Sqrt( ----------------------------------------------------------------- )
sum_i sum_j w_{i,j} |Fobs|_i |Fobs|_j
where
|Fobs| = the observed structure-factor amplitudes
|Fcalc| = the calculated structure-factor amplitudes
G = the scale factor which puts |Fcalc| on the
same scale as |Fobs|
w_{i,j} = the weight for the combination of the reflections
i and j.
sum_i and sum_j are taken over the specified reflections
When the covariance of the amplitudes of reflection i and
reflection j is zero (i.e. the reflections are independent)
w{i,i} can be redefined as w_i and the nested sums collapsed
into one sum.
sum_i w_i(|Fobs|_i - G|Fcalc|_i)^2
RG = Sqrt( ----------------------------------- )
sum_i w_i |Fobs|_i^2
Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510.
refine_analyze.number_disordered_residues
The number of discretely disordered residues in the refined
model.
refine_analyze.occupancy_sum_hydrogen
The sum of the occupancies of the hydrogen atoms in the refined
model.
refine_analyze.occupancy_sum_non_hydrogen
The sum of the occupancies of the non-hydrogen atoms in the
refined model.
refine_analyze.pdbx_Luzzati_d_res_high_obs
record the high resolution for calculating Luzzati statistics.
refine_analyze.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
refine_analyze.pdbx_refine_id
This data item uniquely identifies a refinement within an entry.
attribute pdbx_refine_id in category refine_analyze can be used to distinguish the results
of joint refinements.
refine_funct_minimized
Data items in the REFINE_FUNCT_MINIMIZED category record
details about the individual terms of the function minimized
during refinement.
Example 1 - based on RESTRAIN refinement for the CCP4 test data set
toxd.
<PDBx:refine_funct_minimizedCategory>
<PDBx:refine_funct_minimized pdbx_refine_id="X-ray" type="sum(W*Delta(Amplitude)^2">
<PDBx:number_terms>3009</PDBx:number_terms>
<PDBx:residual>1621.3</PDBx:residual>
</PDBx:refine_funct_minimized>
<PDBx:refine_funct_minimized pdbx_refine_id="X-ray" type="sum(W*Delta(Plane+Rigid)^2">
<PDBx:number_terms>85</PDBx:number_terms>
<PDBx:residual>56.68</PDBx:residual>
</PDBx:refine_funct_minimized>
<PDBx:refine_funct_minimized pdbx_refine_id="X-ray" type="sum(W*Delta(Distance)^2">
<PDBx:number_terms>1219</PDBx:number_terms>
<PDBx:residual>163.59</PDBx:residual>
</PDBx:refine_funct_minimized>
<PDBx:refine_funct_minimized pdbx_refine_id="X-ray" type="sum(W*Delta(U-tempfactors)^2">
<PDBx:number_terms>1192</PDBx:number_terms>
<PDBx:residual>69.338</PDBx:residual>
</PDBx:refine_funct_minimized>
</PDBx:refine_funct_minimizedCategory>
0
1
0
1
0
1
1
1
refine_funct_minimizedCategory
This property indicates that datablock
has a category element refine_funct_minimized.
refine_funct_minimizedItem
Abstract Datatype property for refine_funct_minimized items.
reference_to_refine_funct_minimized
cross-reference to refine_funct_minimized
refine_funct_minimized.number_terms
The number of observations in this term. For example, if the
term is a residual of the X-ray intensities, this item would
contain the number of reflections used in the refinement.
refine_funct_minimized.residual
The residual for this term of the function that was minimized
during the refinement.
refine_funct_minimized.weight
The weight applied to this term of the function that was
minimized during the refinement.
refine_funct_minimized.pdbx_refine_id
This data item uniquely identifies a refinement within an entry.
attribute pdbx_refine_id in category refine_funct_minimized can be used to distinguish the results
of joint refinements.
refine_funct_minimized.type
The type of the function being minimized.
refine_hist
Data items in the REFINE_HIST category record details about the
steps during the refinement of the structure.
These data items are not meant to be as thorough a description
of the refinement as is provided for the final model in other
categories; rather, these data items provide a mechanism for
sketching out the progress of the refinement, supported by a
small set of representative statistics.
Example 1 - based on laboratory records for the collagen-like
peptide [(POG)4 EKG (POG)5]3.
<PDBx:refine_histCategory>
<PDBx:refine_hist cycle_id="C134" pdbx_refine_id="X-ray">
<PDBx:R_factor_R_free>.274</PDBx:R_factor_R_free>
<PDBx:R_factor_R_work>.160</PDBx:R_factor_R_work>
<PDBx:R_factor_all>.265</PDBx:R_factor_all>
<PDBx:R_factor_obs>.195</PDBx:R_factor_obs>
<PDBx:d_res_high>1.85</PDBx:d_res_high>
<PDBx:d_res_low>20.0</PDBx:d_res_low>
<PDBx:details> Add majority of solvent molecules. B factors refined by
group. Continued to remove misplaced water molecules.</PDBx:details>
<PDBx:number_atoms_solvent>217</PDBx:number_atoms_solvent>
<PDBx:number_atoms_total>808</PDBx:number_atoms_total>
<PDBx:number_reflns_R_free>476</PDBx:number_reflns_R_free>
<PDBx:number_reflns_R_work>4410</PDBx:number_reflns_R_work>
<PDBx:number_reflns_all>6174</PDBx:number_reflns_all>
<PDBx:number_reflns_obs>4886</PDBx:number_reflns_obs>
</PDBx:refine_hist>
</PDBx:refine_histCategory>
0
1
0
1
0
1
0
1
1
1
1
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
refine_histCategory
This property indicates that datablock
has a category element refine_hist.
refine_histItem
Abstract Datatype property for refine_hist items.
reference_to_refine_hist
cross-reference to refine_hist
refine_hist.R_factor_R_free
Residual factor R for reflections that satisfy the resolution
limits established by attribute d_res_high in category refine_hist and
attribute d_res_low in category refine_hist and the observation limit
established by attribute observed_criterion in category reflns, and that were used
as the test reflections (i.e. were excluded from the refinement)
when the refinement included the calculation of a 'free'
R factor. Details of how reflections were assigned to the
working and test sets are given in attribute R_free_details.
in category reflns
sum|F~obs~ - F~calc~|
R = ---------------------
sum|F~obs~|
F~obs~ = the observed structure-factor amplitudes
F~calc~ = the calculated structure-factor amplitudes
sum is taken over the specified reflections
refine_hist.R_factor_R_work
Residual factor R for reflections that satisfy the resolution
limits established by attribute d_res_high in category refine_hist and
attribute d_res_low in category refine_hist and the observation limit
established by attribute observed_criterion in category reflns, and that were used
as the working reflections (i.e. were included in the refinement)
when the refinement included the calculation of a 'free'
R factor. Details of how reflections were assigned to the
working and test sets are given in attribute R_free_details.
in category reflns
sum|F~obs~ - F~calc~|
R = ---------------------
sum|F~obs~|
F~obs~ = the observed structure-factor amplitudes
F~calc~ = the calculated structure-factor amplitudes
sum is taken over the specified reflections
refine_hist.R_factor_all
Residual factor R for reflections that satisfy the resolution
limits established by attribute d_res_high in category refine_hist and
attribute d_res_low.
in category refine_hist
sum|F~obs~ - F~calc~|
R = ---------------------
sum|F~obs~|
F~obs~ = the observed structure-factor amplitudes
F~calc~ = the calculated structure-factor amplitudes
sum is taken over the specified reflections
refine_hist.R_factor_obs
Residual factor R for reflections that satisfy the resolution
limits established by attribute d_res_high in category refine_hist and
attribute d_res_low in category refine_hist and the observation criterion
established by attribute observed_criterion.
in category reflns
sum|F~obs~ - F~calc~|
R = ---------------------
sum|F~obs~|
F~obs~ = the observed structure-factor amplitudes
F~calc~ = the calculated structure-factor amplitudes
sum is taken over the specified reflections
refine_hist.d_res_high
The lowest value for the interplanar spacings for the
reflection data for this cycle of refinement. This is called
the highest resolution.
refine_hist.d_res_low
The highest value for the interplanar spacings for the
reflection data for this cycle of refinement. This is
called the lowest resolution.
refine_hist.details
A description of special aspects of this cycle of the refinement
process.
Residues 13-17 fit and added to model;
substantial rebuilding of loop containing
residues 43-48; addition of first atoms to
solvent model; ten cycles of Prolsq
refinement.
refine_hist.number_atoms_solvent
The number of solvent atoms that were included in the model at
this cycle of the refinement.
refine_hist.number_atoms_total
The total number of atoms that were included in the model at
this cycle of the refinement.
refine_hist.number_reflns_R_free
The number of reflections that satisfy the resolution limits
established by attribute d_res_high in category refine_hist and
attribute d_res_low in category refine_hist and the observation limit
established by attribute observed_criterion in category reflns, and that were used
as the test reflections (i.e. were excluded from the refinement)
when the refinement included the calculation of a 'free'
R factor. Details of how reflections were assigned to the
working and test sets are given in attribute R_free_details in category reflns.
refine_hist.number_reflns_R_work
The number of reflections that satisfy the resolution limits
established by attribute d_res_high in category refine_hist and
attribute d_res_low in category refine_hist and the observation limit
established by attribute observed_criterion in category reflns, and that were used
as the working reflections (i.e. were included in the
refinement) when the refinement included the calculation
of a 'free' R factor. Details of how reflections were
assigned to the working and test sets are given in
attribute R_free_details in category reflns.
refine_hist.number_reflns_all
The number of reflections that satisfy the resolution limits
established by attribute d_res_high in category refine_hist and
attribute d_res_low in category refine_hist.
refine_hist.number_reflns_obs
The number of reflections that satisfy the resolution limits
established by attribute d_res_high in category refine_hist and
attribute d_res_low in category refine_hist and the observation criterion
established by attribute observed_criterion in category reflns.
refine_hist.pdbx_number_atoms_carb
Number of carbohydrate atoms included in refinement
refine_hist.pdbx_number_atoms_ligand
Number of ligand atoms included in refinement
refine_hist.pdbx_number_atoms_lipid
Number of lipid atoms included in refinement
refine_hist.pdbx_number_atoms_nucleic_acid
Number of nucleic atoms included in refinement
refine_hist.pdbx_number_atoms_protein
Number of protein atoms included in refinement
refine_hist.pdbx_pseudo_atom_details
Details of pseduo atoms used to model unexplained density
refine_hist.cycle_id
The value of attribute cycle_id in category refine_hist must uniquely identify a
record in the REFINE_HIST list.
Note that this item need not be a number; it can be any unique
identifier.
refine_hist.pdbx_refine_id
This data item uniquely identifies a refinement within an entry.
attribute pdbx_refine_id in category refine_hist can be used to distinguish the results
of joint refinements.
refine_ls_class
Data items in the REFINE_LS_CLASS category record details
about the reflections used for the structure refinement
for each reflection class separately.
Example 1 - data for a modulated structure from van Smaalen
[J. Phys. Condens. Matter (1991), 3, 1247-1263].
<PDBx:refine_ls_classCategory>
<PDBx:refine_ls_class code="Main">
<PDBx:R_factor_gt>0.057</PDBx:R_factor_gt>
</PDBx:refine_ls_class>
<PDBx:refine_ls_class code="Com">
<PDBx:R_factor_gt>0.074</PDBx:R_factor_gt>
</PDBx:refine_ls_class>
<PDBx:refine_ls_class code="NbRefls">
<PDBx:R_factor_gt>0.064</PDBx:R_factor_gt>
</PDBx:refine_ls_class>
<PDBx:refine_ls_class code="LaRefls">
<PDBx:R_factor_gt>0.046</PDBx:R_factor_gt>
</PDBx:refine_ls_class>
<PDBx:refine_ls_class code="Sat1">
<PDBx:R_factor_gt>0.112</PDBx:R_factor_gt>
</PDBx:refine_ls_class>
<PDBx:refine_ls_class code="Sat2">
<PDBx:R_factor_gt>0.177</PDBx:R_factor_gt>
</PDBx:refine_ls_class>
</PDBx:refine_ls_classCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
refine_ls_classCategory
This property indicates that datablock
has a category element refine_ls_class.
refine_ls_classItem
Abstract Datatype property for refine_ls_class items.
reference_to_refine_ls_class
cross-reference to refine_ls_class
refine_ls_class.R_Fsqd_factor
For each reflection class, the residual factor R(F^2^) calculated
on the squared amplitudes of the observed and calculated
structure factors, for the reflections judged significantly
intense (i.e. satisfying the threshold specified by
attribute threshold_expression) in category reflns and included in the refinement.
The reflections also satisfy the resolution limits established
by _refine_ls_class.d_res_high and _refine_ls_class.d_res_low.
sum | F(obs)^2^ - F(calc)^2^ |
R(Fsqd) = -------------------------------
sum F(obs)^2^
F(obs)^2^ = squares of the observed structure-factor amplitudes
F(calc)^2^ = squares of the calculated structure-factor
amplitudes
and the sum is taken over the reflections of this class.
refine_ls_class.R_I_factor
For each reflection class, the residual factor R(I) for the
reflections judged significantly intense (i.e. satisfying the
threshold specified by attribute threshold_expression) in category reflns and
included in the refinement.
This is most often calculated in Rietveld refinements
against powder data, where it is referred to as R~B~ or R~Bragg~
sum | I(obs) - I(calc) |
R(I) = ------------------------
sum | I(obs) |
I(obs) = the net observed intensities
I(calc) = the net calculated intensities
and the sum is taken over the reflections of this class.
refine_ls_class.R_factor_all
For each reflection class, the residual factor for all
reflections satisfying the resolution limits established by
_refine_ls_class.d_res_high and _refine_ls_class.d_res_low.
This is the conventional R factor. See also the
definition of attribute wR_factor_all.
in category refine_ls_class
sum | F(obs) - F(calc) |
R = ------------------------
sum | F(obs) |
F(obs) = the observed structure-factor amplitudes
F(calc) = the calculated structure-factor amplitudes
and the sum is taken over the reflections of this class.
refine_ls_class.R_factor_gt
For each reflection class, the residual factor for significantly
intense reflections (see attribute threshold_expression) in category reflns included
in the refinement.
The reflections also satisfy the resolution limits established by
_refine_ls_class.d_res_high and _refine_ls_class.d_res_low.
This is the conventional R factor. See also the definition of
attribute wR_factor_all.
in category refine_ls_class
sum | F(obs) - F(calc) |
R = ------------------------
sum | F(obs) |
F(obs) = the observed structure-factor amplitudes
F(calc) = the calculated structure-factor amplitudes
and the sum is taken over the reflections of this class.
refine_ls_class.d_res_high
For each reflection class, the lowest value in angstroms
for the interplanar spacings for the reflections used in the
refinement. This is called the highest resolution.
refine_ls_class.d_res_low
For each reflection class, the highest value in angstroms
for the interplanar spacings for the reflections used in the
refinement. This is called the lowest resolution.
refine_ls_class.wR_factor_all
For each reflection class, the weighted residual factor for all
reflections included in the refinement. The reflections also
satisfy the resolution limits established by
_refine_ls_class.d_res_high and _refine_ls_class.d_res_low.
See also the attribute R_factor_ in category refine_ls_class definitions.
( sum w [ Y(obs) - Y(calc) ]^2^ )^1/2^
wR = ( ------------------------------ )
( sum w Y(obs)^2^ )
Y(obs) = the observed amplitude specified by
attribute ls_structure_factor_coef
in category refine Y(calc) = the calculated amplitude specified by
attribute ls_structure_factor_coef
in category refine w = the least-squares weight
and the sum is taken over the reflections of this class.
refine_ls_class.code
The code identifying a certain reflection class. This code must
match a attribute code in category reflns_class.
1
m1
s2
refine_ls_restr
Data items in the REFINE_LS_RESTR category record details about
the restraints applied to various classes of parameters during
the least-squares refinement.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:refine_ls_restrCategory>
<PDBx:refine_ls_restr type="bond_d">
<PDBx:criterion>> 2\s</PDBx:criterion>
<PDBx:dev_ideal>0.018</PDBx:dev_ideal>
<PDBx:dev_ideal_target>0.020</PDBx:dev_ideal_target>
<PDBx:number>1654</PDBx:number>
<PDBx:pdbx_refine_id>X-ray</PDBx:pdbx_refine_id>
<PDBx:rejects>22</PDBx:rejects>
</PDBx:refine_ls_restr>
<PDBx:refine_ls_restr type="angle_d">
<PDBx:criterion>> 2\s</PDBx:criterion>
<PDBx:dev_ideal>0.038</PDBx:dev_ideal>
<PDBx:dev_ideal_target>0.030</PDBx:dev_ideal_target>
<PDBx:number>2246</PDBx:number>
<PDBx:pdbx_refine_id>X-ray</PDBx:pdbx_refine_id>
<PDBx:rejects>139</PDBx:rejects>
</PDBx:refine_ls_restr>
<PDBx:refine_ls_restr type="planar_d">
<PDBx:criterion>> 2\s</PDBx:criterion>
<PDBx:dev_ideal>0.043</PDBx:dev_ideal>
<PDBx:dev_ideal_target>0.040</PDBx:dev_ideal_target>
<PDBx:number>498</PDBx:number>
<PDBx:pdbx_refine_id>X-ray</PDBx:pdbx_refine_id>
<PDBx:rejects>21</PDBx:rejects>
</PDBx:refine_ls_restr>
<PDBx:refine_ls_restr type="planar">
<PDBx:criterion>> 2\s</PDBx:criterion>
<PDBx:dev_ideal>0.015</PDBx:dev_ideal>
<PDBx:dev_ideal_target>0.020</PDBx:dev_ideal_target>
<PDBx:number>270</PDBx:number>
<PDBx:pdbx_refine_id>X-ray</PDBx:pdbx_refine_id>
<PDBx:rejects>1</PDBx:rejects>
</PDBx:refine_ls_restr>
<PDBx:refine_ls_restr type="chiral">
<PDBx:criterion>> 2\s</PDBx:criterion>
<PDBx:dev_ideal>0.177</PDBx:dev_ideal>
<PDBx:dev_ideal_target>0.150</PDBx:dev_ideal_target>
<PDBx:number>278</PDBx:number>
<PDBx:pdbx_refine_id>X-ray</PDBx:pdbx_refine_id>
<PDBx:rejects>2</PDBx:rejects>
</PDBx:refine_ls_restr>
<PDBx:refine_ls_restr type="singtor_nbd">
<PDBx:criterion>> 2\s</PDBx:criterion>
<PDBx:dev_ideal>0.216</PDBx:dev_ideal>
<PDBx:dev_ideal_target>0.500</PDBx:dev_ideal_target>
<PDBx:number>582</PDBx:number>
<PDBx:pdbx_refine_id>X-ray</PDBx:pdbx_refine_id>
<PDBx:rejects>0</PDBx:rejects>
</PDBx:refine_ls_restr>
<PDBx:refine_ls_restr type="multtor_nbd">
<PDBx:criterion>> 2\s</PDBx:criterion>
<PDBx:dev_ideal>0.207</PDBx:dev_ideal>
<PDBx:dev_ideal_target>0.500</PDBx:dev_ideal_target>
<PDBx:number>419</PDBx:number>
<PDBx:pdbx_refine_id>X-ray</PDBx:pdbx_refine_id>
<PDBx:rejects>0</PDBx:rejects>
</PDBx:refine_ls_restr>
<PDBx:refine_ls_restr type="xyhbond_nbd">
<PDBx:criterion>> 2\s</PDBx:criterion>
<PDBx:dev_ideal>0.245</PDBx:dev_ideal>
<PDBx:dev_ideal_target>0.500</PDBx:dev_ideal_target>
<PDBx:number>149</PDBx:number>
<PDBx:pdbx_refine_id>X-ray</PDBx:pdbx_refine_id>
<PDBx:rejects>0</PDBx:rejects>
</PDBx:refine_ls_restr>
<PDBx:refine_ls_restr type="planar_tor">
<PDBx:criterion>> 2\s</PDBx:criterion>
<PDBx:dev_ideal>2.6</PDBx:dev_ideal>
<PDBx:dev_ideal_target>3.0</PDBx:dev_ideal_target>
<PDBx:number>203</PDBx:number>
<PDBx:pdbx_refine_id>X-ray</PDBx:pdbx_refine_id>
<PDBx:rejects>9</PDBx:rejects>
</PDBx:refine_ls_restr>
<PDBx:refine_ls_restr type="staggered_tor">
<PDBx:criterion>> 2\s</PDBx:criterion>
<PDBx:dev_ideal>17.4</PDBx:dev_ideal>
<PDBx:dev_ideal_target>15.0</PDBx:dev_ideal_target>
<PDBx:number>298</PDBx:number>
<PDBx:pdbx_refine_id>X-ray</PDBx:pdbx_refine_id>
<PDBx:rejects>31</PDBx:rejects>
</PDBx:refine_ls_restr>
<PDBx:refine_ls_restr type="orthonormal_tor">
<PDBx:criterion>> 2\s</PDBx:criterion>
<PDBx:dev_ideal>18.1</PDBx:dev_ideal>
<PDBx:dev_ideal_target>20.0</PDBx:dev_ideal_target>
<PDBx:number>12</PDBx:number>
<PDBx:pdbx_refine_id>X-ray</PDBx:pdbx_refine_id>
<PDBx:rejects>1</PDBx:rejects>
</PDBx:refine_ls_restr>
</PDBx:refine_ls_restrCategory>
0
1
0
1
0
1
0
1
1
1
0
1
0
1
0
1
1
refine_ls_restrCategory
This property indicates that datablock
has a category element refine_ls_restr.
refine_ls_restrItem
Abstract Datatype property for refine_ls_restr items.
reference_to_refine_ls_restr
cross-reference to refine_ls_restr
refine_ls_restr.criterion
A criterion used to define a parameter value that deviates
significantly from its ideal value in the model obtained by
restrained least-squares refinement.
> 3\s
refine_ls_restr.dev_ideal
For the given parameter type, the root-mean-square deviation
between the ideal values used as restraints in the least-squares
refinement and the values obtained by refinement. For instance,
bond distances may deviate by 0.018 \%A (r.m.s.) from ideal
values in the current model.
refine_ls_restr.dev_ideal_target
For the given parameter type, the target root-mean-square
deviation between the ideal values used as restraints in the
least-squares refinement and the values obtained by refinement.
refine_ls_restr.number
The number of parameters of this type subjected to restraint in
least-squares refinement.
refine_ls_restr.pdbx_refine_id
This data item uniquely identifies a refinement within an entry.
attribute pdbx_refine_id in category refine_ls_restr can be used to distinguish the results
of joint refinements.
refine_ls_restr.pdbx_restraint_function
The functional form of the restraint function used in the least-squares
refinement.
SINUSOIDAL
HARMONIC
SEMIHARMONIC
refine_ls_restr.rejects
The number of parameters of this type that deviate from ideal
values by more than the amount defined in
attribute criterion in category refine_ls_restr in the model obtained by restrained
least-squares refinement.
refine_ls_restr.weight
The weighting value applied to this type of restraint in
the least-squares refinement.
refine_ls_restr.type
The type of the parameter being restrained.
Explicit sets of data values are provided for the programs
PROTIN/PROLSQ (beginning with p_) and RESTRAIN (beginning with
RESTRAIN_). As computer programs change, these data values
are given as examples, not as an enumeration list. Computer
programs that convert a data block to a refinement table will
expect the exact form of the data values given here to be used.
bond distance
p_bond_d
bond angle expressed as a distance
p_angle_d
planar 1,4 distance
p_planar_d
X-H bond distance
p_xhbond_d
X-H bond angle expressed as a distance
p_xhangle_d
hydrogen distance
p_hydrog_d
special distance
p_special_d
planes
p_planar
chiral centres
p_chiral
single-torsion non-bonded contact
p_singtor_nbd
multiple-torsion non-bonded contact
p_multtor_nbd
possible (X...Y) hydrogen bond
p_xyhbond_nbd
possible (X-H...Y) hydrogen bond
p_xhyhbond_nbd
special torsion angle
p_special_tor
planar torsion angle
p_planar_tor
staggered torsion angle
p_staggered_tor
orthonormal torsion angle
p_orthonormal_tor
main-chain bond isotropic displacement parameter
p_mcbond_it
main-chain angle isotropic displacement parameter
p_mcangle_it
side-chain bond isotropic displacement parameter
p_scbond_it
side-chain angle isotropic displacement parameter
p_scangle_it
X-H bond isotropic displacement parameter
p_xhbond_it
X-H angle isotropic displacement parameter
p_xhangle_it
special isotropic displacement parameter
p_special_it
The root-mean-square deviation
of the difference between the values calculated from the structures
used to compile the restraints dictionary parameters and the dictionary
values themselves in the distance range less than 2.12 Angstroms.
RESTRAIN_Distances < 2.12
The root-mean-square deviation
of the difference between the values calculated from the structures
used to compile the restraints dictionary parameters and the dictionary
values themselves in the distance range 2.12 - 2.625 Angstroms.
RESTRAIN_Distances 2.12 < D < 2.625
The root-mean-square deviation
of the difference between the values calculated from the structures
used to compile the restraints dictionary parameters and the dictionary
values themselves in the distance range greater than 2.625 Angstroms.
RESTRAIN_Distances > 2.625
The root-mean-square deviation
of the difference between the values calculated from the structures
used to compile the restraints dictionary parameters and the dictionary
values themselves for peptide planes.
RESTRAIN_Peptide Planes
The root-mean-square deviation
of the difference between the values calculated from the structures
used to compile the restraints dictionary parameters and the dictionary
values themselves for rings and planes other than peptide planes.
RESTRAIN_Ring and other planes
RESTRAIN_rms diffs for Uiso atoms at dist 1.2-1.4
RESTRAIN_rms diffs for Uiso atoms at dist 1.4-1.6
RESTRAIN_rms diffs for Uiso atoms at dist 1.8-2.0
RESTRAIN_rms diffs for Uiso atoms at dist 2.0-2.2
RESTRAIN_rms diffs for Uiso atoms at dist 2.2-2.4
RESTRAIN_rms diffs for Uiso atoms at dist >2.4
refine_ls_restr_ncs
Data items in the REFINE_LS_RESTR_NCS category record details
about the restraints applied to atom positions in domains
related by noncrystallographic symmetry during least-squares
refinement, and also about the deviation of the restrained
atomic parameters at the end of the refinement. It is
expected that these values will only be reported once for each
set of restrained domains.
Example 1 - based on laboratory records for the collagen-like
peptide, HYP-.
<PDBx:refine_ls_restr_ncsCategory>
<PDBx:refine_ls_restr_ncs pdbx_ordinal="1">
<PDBx:dom_id>d2</PDBx:dom_id>
<PDBx:ncs_model_details>
NCS restraint for pseudo-twofold symmetry between domains
d1 and d2. Position weight coefficient given in
Kcal/(mol \%A^2^) and isotropic B weight coefficient given
in \%A^2^.</PDBx:ncs_model_details>
<PDBx:pdbx_asym_id>A</PDBx:pdbx_asym_id>
<PDBx:pdbx_ens_id>1</PDBx:pdbx_ens_id>
<PDBx:pdbx_refine_id>X-ray</PDBx:pdbx_refine_id>
<PDBx:pdbx_type>medium positional</PDBx:pdbx_type>
<PDBx:rms_dev_B_iso>0.16</PDBx:rms_dev_B_iso>
<PDBx:rms_dev_position>0.09</PDBx:rms_dev_position>
<PDBx:weight_B_iso>2.0</PDBx:weight_B_iso>
<PDBx:weight_position>300.0</PDBx:weight_position>
</PDBx:refine_ls_restr_ncs>
</PDBx:refine_ls_restr_ncsCategory>
1
1
0
1
0
1
1
1
1
1
0
1
1
1
0
1
1
1
0
1
0
1
0
1
0
1
0
1
1
refine_ls_restr_ncsCategory
This property indicates that datablock
has a category element refine_ls_restr_ncs.
refine_ls_restr_ncsItem
Abstract Datatype property for refine_ls_restr_ncs items.
reference_to_refine_ls_restr_ncs
cross-reference to refine_ls_restr_ncs
refine_ls_restr_ncs.dom_id
This data item is a pointer to attribute id in category struct_ncs_dom in the
STRUCT_NCS_DOM category.
refine_ls_restr_ncs.ncs_model_details
Special aspects of the manner in which noncrystallographic
restraints were applied to atomic parameters in the domain
specified by attribute dom_id in category refine_ls_restr_ncs and equivalent
atomic parameters in the domains against which it was restrained.
refine_ls_restr_ncs.pdbx_asym_id
A reference to attribute id in category struct_asym.
refine_ls_restr_ncs.pdbx_auth_asym_id
A reference to the PDB Chain ID
refine_ls_restr_ncs.pdbx_ens_id
This is a unique identifier for a collection NCS related domains.
This references item '_struct_ncs_dom.pdbx_ens_id'.
refine_ls_restr_ncs.pdbx_number
record the residue number .
refine_ls_restr_ncs.pdbx_refine_id
This data item uniquely identifies a refinement within an entry.
attribute pdbx_refine_id in category refine_ls_restr_ncs can be used to distinguish the results
of joint refinements.
refine_ls_restr_ncs.pdbx_rms
record the standard divation between one segment to another
refine_ls_restr_ncs.pdbx_type
The type of NCS restraint. (for example: tight positional)
refine_ls_restr_ncs.pdbx_weight
record the weight used for NCS restraint.
refine_ls_restr_ncs.rms_dev_B_iso
The root-mean-square deviation in equivalent isotropic
displacement parameters in the domain specified by
attribute dom_id
in category refine_ls_restr_ncs and in the domains against which it was restrained.
refine_ls_restr_ncs.rms_dev_position
The root-mean-square deviation in equivalent atom positions in
the domain specified by attribute dom_id in category refine_ls_restr_ncs and in the
domains against which it was restrained.
refine_ls_restr_ncs.weight_B_iso
The value of the weighting coefficient used in
noncrystallographic symmetry restraint of isotropic displacement
parameters in the domain specified by
attribute dom_id in category refine_ls_restr_ncs to equivalent isotropic
displacement parameters in the domains against
which it was restrained.
refine_ls_restr_ncs.weight_position
The value of the weighting coefficient used in
noncrystallographic symmetry restraint of atom positions in the
domain specified by attribute dom_id in category refine_ls_restr_ncs to equivalent
atom positions in the domains against which it was restrained.
refine_ls_restr_ncs.pdbx_ordinal
An ordinal index for the list of NCS restraints.
refine_ls_restr_type
Data items in the REFINE_LS_RESTR_TYPE category record details
about the restraint types used in the least-squares refinement.
Example 1 - based on RESTRAIN refinement for the CCP4 test data set
toxd.
<PDBx:refine_ls_restrCategory>
<PDBx:refine_ls_restr type="RESTRAIN_Distances < 2.12">
<PDBx:dev_ideal>0.005</PDBx:dev_ideal>
<PDBx:dev_ideal_target>0.022</PDBx:dev_ideal_target>
<PDBx:number>509</PDBx:number>
</PDBx:refine_ls_restr>
<PDBx:refine_ls_restr type="RESTRAIN_Distances 2.12 < D < 2.625">
<PDBx:dev_ideal>0.016</PDBx:dev_ideal>
<PDBx:dev_ideal_target>0.037</PDBx:dev_ideal_target>
<PDBx:number>671</PDBx:number>
</PDBx:refine_ls_restr>
<PDBx:refine_ls_restr type="RESTRAIN_Distances > 2.625">
<PDBx:dev_ideal>0.034</PDBx:dev_ideal>
<PDBx:dev_ideal_target>0.043</PDBx:dev_ideal_target>
<PDBx:number>39</PDBx:number>
</PDBx:refine_ls_restr>
<PDBx:refine_ls_restr type="RESTRAIN_Peptide Planes">
<PDBx:dev_ideal>0.002</PDBx:dev_ideal>
<PDBx:dev_ideal_target>0.010</PDBx:dev_ideal_target>
<PDBx:number>59</PDBx:number>
</PDBx:refine_ls_restr>
<PDBx:refine_ls_restr type="RESTRAIN_Ring and other planes">
<PDBx:dev_ideal>0.014</PDBx:dev_ideal>
<PDBx:dev_ideal_target>0.010</PDBx:dev_ideal_target>
<PDBx:number>26</PDBx:number>
</PDBx:refine_ls_restr>
<PDBx:refine_ls_restr type="RESTRAIN_rms diffs for Uiso atoms at dist 1.2-1.4">
<PDBx:dev_ideal>0.106</PDBx:dev_ideal>
<PDBx:dev_ideal_target></PDBx:dev_ideal_target>
<PDBx:number>212</PDBx:number>
</PDBx:refine_ls_restr>
<PDBx:refine_ls_restr type="RESTRAIN_rms diffs for Uiso atoms at dist 1.4-1.6">
<PDBx:dev_ideal>0.101</PDBx:dev_ideal>
<PDBx:dev_ideal_target></PDBx:dev_ideal_target>
<PDBx:number>288</PDBx:number>
</PDBx:refine_ls_restr>
<PDBx:refine_ls_restr type="RESTRAIN_rms diffs for Uiso atoms at dist 1.8-2.0">
<PDBx:dev_ideal>0.077</PDBx:dev_ideal>
<PDBx:dev_ideal_target></PDBx:dev_ideal_target>
<PDBx:number>6</PDBx:number>
</PDBx:refine_ls_restr>
<PDBx:refine_ls_restr type="RESTRAIN_rms diffs for Uiso atoms at dist 2.0-2.2">
<PDBx:dev_ideal>0.114</PDBx:dev_ideal>
<PDBx:dev_ideal_target></PDBx:dev_ideal_target>
<PDBx:number>10</PDBx:number>
</PDBx:refine_ls_restr>
<PDBx:refine_ls_restr type="RESTRAIN_rms diffs for Uiso atoms at dist 2.2-2.4">
<PDBx:dev_ideal>0.119</PDBx:dev_ideal>
<PDBx:dev_ideal_target></PDBx:dev_ideal_target>
<PDBx:number>215</PDBx:number>
</PDBx:refine_ls_restr>
<PDBx:refine_ls_restr type="RESTRAIN_rms diffs for Uiso atoms at dist >2.4">
<PDBx:dev_ideal>0.106</PDBx:dev_ideal>
<PDBx:dev_ideal_target></PDBx:dev_ideal_target>
<PDBx:number>461</PDBx:number>
</PDBx:refine_ls_restr>
</PDBx:refine_ls_restrCategory>
<PDBx:refine_ls_restr_typeCategory>
<PDBx:refine_ls_restr_type type="RESTRAIN_Distances < 2.12">
<PDBx:distance_cutoff_high>2.12</PDBx:distance_cutoff_high>
<PDBx:distance_cutoff_low></PDBx:distance_cutoff_low>
</PDBx:refine_ls_restr_type>
<PDBx:refine_ls_restr_type type="RESTRAIN_Distances 2.12 < D < 2.625">
<PDBx:distance_cutoff_high>2.625</PDBx:distance_cutoff_high>
<PDBx:distance_cutoff_low>2.12</PDBx:distance_cutoff_low>
</PDBx:refine_ls_restr_type>
<PDBx:refine_ls_restr_type type="RESTRAIN_Distances > 2.625">
<PDBx:distance_cutoff_high></PDBx:distance_cutoff_high>
<PDBx:distance_cutoff_low>2.625</PDBx:distance_cutoff_low>
</PDBx:refine_ls_restr_type>
<PDBx:refine_ls_restr_type type="RESTRAIN_Peptide Planes">
<PDBx:distance_cutoff_high></PDBx:distance_cutoff_high>
<PDBx:distance_cutoff_low></PDBx:distance_cutoff_low>
</PDBx:refine_ls_restr_type>
<PDBx:refine_ls_restr_type type="RESTRAIN_Ring and other planes">
<PDBx:distance_cutoff_high></PDBx:distance_cutoff_high>
<PDBx:distance_cutoff_low></PDBx:distance_cutoff_low>
</PDBx:refine_ls_restr_type>
<PDBx:refine_ls_restr_type type="RESTRAIN_rms diffs for Uiso atoms at dist 1.2-1.4">
<PDBx:distance_cutoff_high>1.4</PDBx:distance_cutoff_high>
<PDBx:distance_cutoff_low>1.2</PDBx:distance_cutoff_low>
</PDBx:refine_ls_restr_type>
<PDBx:refine_ls_restr_type type="RESTRAIN_rms diffs for Uiso atoms at dist 1.4-1.6">
<PDBx:distance_cutoff_high>1.6</PDBx:distance_cutoff_high>
<PDBx:distance_cutoff_low>1.4</PDBx:distance_cutoff_low>
</PDBx:refine_ls_restr_type>
<PDBx:refine_ls_restr_type type="RESTRAIN_rms diffs for Uiso atoms at dist 1.8-2.0">
<PDBx:distance_cutoff_high>2.0</PDBx:distance_cutoff_high>
<PDBx:distance_cutoff_low>1.8</PDBx:distance_cutoff_low>
</PDBx:refine_ls_restr_type>
<PDBx:refine_ls_restr_type type="RESTRAIN_rms diffs for Uiso atoms at dist 2.0-2.2">
<PDBx:distance_cutoff_high>2.2</PDBx:distance_cutoff_high>
<PDBx:distance_cutoff_low>2.0</PDBx:distance_cutoff_low>
</PDBx:refine_ls_restr_type>
<PDBx:refine_ls_restr_type type="RESTRAIN_rms diffs for Uiso atoms at dist 2.2-2.4">
<PDBx:distance_cutoff_high>2.4</PDBx:distance_cutoff_high>
<PDBx:distance_cutoff_low>2.2</PDBx:distance_cutoff_low>
</PDBx:refine_ls_restr_type>
<PDBx:refine_ls_restr_type type="RESTRAIN_rms diffs for Uiso atoms at dist >2.4">
<PDBx:distance_cutoff_high></PDBx:distance_cutoff_high>
<PDBx:distance_cutoff_low>2.4</PDBx:distance_cutoff_low>
</PDBx:refine_ls_restr_type>
</PDBx:refine_ls_restr_typeCategory>
0
1
0
1
1
refine_ls_restr_typeCategory
This property indicates that datablock
has a category element refine_ls_restr_type.
refine_ls_restr_typeItem
Abstract Datatype property for refine_ls_restr_type items.
reference_to_refine_ls_restr_type
cross-reference to refine_ls_restr_type
refine_ls_restr_type.distance_cutoff_high
The upper limit in angstroms of the distance range applied to
the current restraint type.
refine_ls_restr_type.distance_cutoff_low
The lower limit in angstroms of the distance range applied to
the current restraint type.
refine_ls_restr_type.type
This data item is a pointer to attribute type in category refine_ls_restr in the
REFINE_LS_RESTR category.
refine_ls_shell
Data items in the REFINE_LS_SHELL category record details about
the results of the least-squares refinement broken down into
shells of resolution.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:refine_ls_shellCategory>
<PDBx:refine_ls_shell d_res_high="4.51" pdbx_refine_id="X-ray">
<PDBx:R_factor_obs>0.196</PDBx:R_factor_obs>
<PDBx:d_res_low>8.00</PDBx:d_res_low>
<PDBx:number_reflns_obs>1226</PDBx:number_reflns_obs>
</PDBx:refine_ls_shell>
<PDBx:refine_ls_shell d_res_high="3.48" pdbx_refine_id="X-ray">
<PDBx:R_factor_obs>0.146</PDBx:R_factor_obs>
<PDBx:d_res_low>4.51</PDBx:d_res_low>
<PDBx:number_reflns_obs>1679</PDBx:number_reflns_obs>
</PDBx:refine_ls_shell>
<PDBx:refine_ls_shell d_res_high="2.94" pdbx_refine_id="X-ray">
<PDBx:R_factor_obs>0.160</PDBx:R_factor_obs>
<PDBx:d_res_low>3.48</PDBx:d_res_low>
<PDBx:number_reflns_obs>2014</PDBx:number_reflns_obs>
</PDBx:refine_ls_shell>
<PDBx:refine_ls_shell d_res_high="2.59" pdbx_refine_id="X-ray">
<PDBx:R_factor_obs>0.182</PDBx:R_factor_obs>
<PDBx:d_res_low>2.94</PDBx:d_res_low>
<PDBx:number_reflns_obs>2147</PDBx:number_reflns_obs>
</PDBx:refine_ls_shell>
<PDBx:refine_ls_shell d_res_high="2.34" pdbx_refine_id="X-ray">
<PDBx:R_factor_obs>0.193</PDBx:R_factor_obs>
<PDBx:d_res_low>2.59</PDBx:d_res_low>
<PDBx:number_reflns_obs>2127</PDBx:number_reflns_obs>
</PDBx:refine_ls_shell>
<PDBx:refine_ls_shell d_res_high="2.15" pdbx_refine_id="X-ray">
<PDBx:R_factor_obs>0.203</PDBx:R_factor_obs>
<PDBx:d_res_low>2.34</PDBx:d_res_low>
<PDBx:number_reflns_obs>2061</PDBx:number_reflns_obs>
</PDBx:refine_ls_shell>
<PDBx:refine_ls_shell d_res_high="2.00" pdbx_refine_id="X-ray">
<PDBx:R_factor_obs>0.188</PDBx:R_factor_obs>
<PDBx:d_res_low>2.15</PDBx:d_res_low>
<PDBx:number_reflns_obs>1647</PDBx:number_reflns_obs>
</PDBx:refine_ls_shell>
</PDBx:refine_ls_shellCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
refine_ls_shellCategory
This property indicates that datablock
has a category element refine_ls_shell.
refine_ls_shellItem
Abstract Datatype property for refine_ls_shell items.
reference_to_refine_ls_shell
cross-reference to refine_ls_shell
refine_ls_shell.R_factor_R_free
Residual factor R for reflections that satisfy the resolution
limits established by attribute d_res_high in category refine_ls_shell and
attribute d_res_low in category refine_ls_shell and the observation limit
established by attribute observed_criterion in category reflns, and that were
used as the test reflections (i.e. were excluded from the
refinement) when the refinement included the calculation
of a 'free' R factor. Details of how reflections were assigned
to the working and test sets are given in attribute R_free_details.
in category reflns
sum|F~obs~ - F~calc~|
R = ---------------------
sum|F~obs~|
F~obs~ = the observed structure-factor amplitudes
F~calc~ = the calculated structure-factor amplitudes
sum is taken over the specified reflections
refine_ls_shell.R_factor_R_free_error
The estimated error in attribute R_factor_R_free.
in category refine_ls_shell The method used to estimate the error is described in the
item attribute ls_R_factor_R_free_error_details in category refine.
refine_ls_shell.R_factor_R_work
Residual factor R for reflections that satisfy the resolution
limits established by attribute d_res_high in category refine_ls_shell and
attribute d_res_low in category refine_ls_shell and the observation limit
established by attribute observed_criterion in category reflns, and that were used
as the working reflections (i.e. were included in the
refinement) when the refinement included the calculation of
a 'free' R factor. Details of how reflections were assigned
to the working and test sets are given in attribute R_free_details.
in category reflns
sum|F~obs~ - F~calc~|
R = ---------------------
sum|F~obs~|
F~obs~ = the observed structure-factor amplitudes
F~calc~ = the calculated structure-factor amplitudes
sum is taken over the specified reflections
refine_ls_shell.R_factor_all
Residual factor R for reflections that satisfy the resolution
limits established by attribute d_res_high in category refine_ls_shell and
attribute d_res_low.
in category refine_ls_shell
sum|F~obs~ - F~calc~|
R = ---------------------
sum|F~obs~|
F~obs~ = the observed structure-factor amplitudes
F~calc~ = the calculated structure-factor amplitudes
sum is taken over the specified reflections
refine_ls_shell.R_factor_obs
Residual factor R for reflections that satisfy the resolution
limits established by attribute d_res_high in category refine_ls_shell and
attribute d_res_low in category refine_ls_shell and the observation criterion
established by attribute observed_criterion.
in category reflns
sum|F~obs~ - F~calc~|
R = ---------------------
sum|F~obs~|
F~obs~ = the observed structure-factor amplitudes
F~calc~ = the calculated structure-factor amplitudes
sum is taken over the specified reflections
refine_ls_shell.d_res_low
The highest value for the interplanar spacings for the
reflection data in this shell. This is called the lowest
resolution.
refine_ls_shell.number_reflns_R_free
The number of reflections that satisfy the resolution limits
established by attribute d_res_high in category refine_ls_shell and
attribute d_res_low in category refine_ls_shell and the observation limit
established by attribute observed_criterion in category reflns, and that were used
as the test reflections (i.e. were excluded from the refinement)
when the refinement included the calculation of a 'free'
R factor. Details of how reflections were assigned to the
working and test sets are given in attribute R_free_details in category reflns.
refine_ls_shell.number_reflns_R_work
The number of reflections that satisfy the resolution limits
established by attribute d_res_high in category refine_ls_shell and
attribute d_res_low in category refine_ls_shell and the observation limit
established by attribute observed_criterion in category reflns, and that were used
as the working reflections (i.e. were included in the
refinement) when the refinement included the calculation of
a 'free' R factor. Details of how reflections were assigned
to the working and test sets are given in attribute R_free_details in category reflns.
refine_ls_shell.number_reflns_all
The number of reflections that satisfy the resolution limits
established by attribute d_res_high in category refine_ls_shell and
attribute d_res_low in category refine_ls_shell.
refine_ls_shell.number_reflns_obs
The number of reflections that satisfy the resolution limits
established by attribute d_res_high in category refine_ls_shell and
attribute d_res_low in category refine_ls_shell and the observation criterion
established by attribute observed_criterion in category reflns.
refine_ls_shell.pdbx_phase_error
The average phase error for all reflections in the resolution shell.
0.30
refine_ls_shell.pdbx_total_number_of_bins_used
Total number of bins used.
refine_ls_shell.percent_reflns_R_free
The number of reflections that satisfy the resolution limits
established by attribute d_res_high in category refine_ls_shell and
attribute d_res_low in category refine_ls_shell and the observation limit
established by attribute observed_criterion in category reflns, and that were used
as the test reflections (i.e. were excluded from the refinement)
when the refinement included the calculation of a 'free'
R factor, expressed as a percentage of the number of
geometrically observable reflections that satisfy the
reflection limits.
refine_ls_shell.percent_reflns_obs
The number of reflections that satisfy the resolution limits
established by attribute d_res_high in category refine_ls_shell and
attribute d_res_low in category refine_ls_shell and the observation criterion
established by attribute observed_criterion in category reflns, expressed as a
percentage of the number of geometrically observable
reflections that satisfy the resolution limits.
refine_ls_shell.redundancy_reflns_all
The ratio of the total number of observations of the reflections
that satisfy the resolution limits established by
_refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low
to the number of crystallographically unique reflections that
satisfy the same limits.
refine_ls_shell.redundancy_reflns_obs
The ratio of the total number of observations of the
reflections that satisfy the resolution limits established by
_refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and
the observation criterion established by
attribute observed_criterion in category reflns to the number of crystallographically
unique reflections that satisfy the same limits.
refine_ls_shell.wR_factor_R_free
Weighted residual factor wR for reflections that satisfy the
resolution limits established by attribute d_res_high
in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation limit
established by attribute observed_criterion in category reflns, and that were used
as the test reflections (i.e. were excluded from the refinement)
when the refinement included the calculation of a 'free'
R factor. Details of how reflections were assigned to the
working and test sets are given in attribute R_free_details.
in category reflns
( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^
wR = ( ---------------------------- )
( sum|w Y~obs~^2^| )
Y~obs~ = the observed amplitude specified by
attribute ls_structure_factor_coef
in category refine Y~calc~ = the calculated amplitude specified by
attribute ls_structure_factor_coef
in category refine w = the least-squares weight
sum is taken over the specified reflections
refine_ls_shell.wR_factor_R_work
Weighted residual factor wR for reflections that satisfy the
resolution limits established by attribute d_res_high
in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation limit
established by attribute observed_criterion in category reflns, and that were used
as the working reflections (i.e. were included in the
refinement) when the refinement included the calculation of
a 'free' R factor. Details of how reflections were assigned
to the working and test sets are given in attribute R_free_details.
in category reflns
( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^
wR = ( ---------------------------- )
( sum|w Y~obs~^2^| )
Y~obs~ = the observed amplitude specified by
attribute ls_structure_factor_coef
in category refine Y~calc~ = the calculated amplitude specified by
attribute ls_structure_factor_coef
in category refine w = the least-squares weight
sum is taken over the specified reflections
refine_ls_shell.wR_factor_all
Weighted residual factor wR for reflections that satisfy the
resolution limits established by attribute d_res_high
in category refine_ls_shell and attribute d_res_low.
in category refine_ls_shell
( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^
wR = ( ---------------------------- )
( sum|w Y~obs~^2^| )
Y~obs~ = the observed amplitude specified by
attribute ls_structure_factor_coef
in category refine Y~calc~ = the calculated amplitude specified by
attribute ls_structure_factor_coef
in category refine w = the least-squares weight
sum is taken over the specified reflections
refine_ls_shell.wR_factor_obs
Weighted residual factor wR for reflections that satisfy the
resolution limits established by attribute d_res_high
in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation criterion
established by attribute observed_criterion.
in category reflns
( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^
wR = ( ---------------------------- )
( sum|w Y~obs~^2^| )
Y~obs~ = the observed amplitude specified by
attribute ls_structure_factor_coef
in category refine Y~calc~ = the calculated amplitude specified by
attribute ls_structure_factor_coef
in category refine w = the least-squares weight
sum is taken over the specified reflections
refine_ls_shell.d_res_high
The lowest value for the interplanar spacings for the
reflection data in this shell. This is called
the highest resolution.
refine_ls_shell.pdbx_refine_id
This data item uniquely identifies a refinement within an entry.
attribute pdbx_refine_id in category refine_ls_shell can be used to distinguish the results
of joint refinements.
refine_occupancy
Data items in the REFINE_OCCUPANCY category record details
about the treatment of atom occupancies during refinement.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:refine_occupancyCategory>
<PDBx:refine_occupancy class="protein" pdbx_refine_id="X-ray">
<PDBx:details></PDBx:details>
<PDBx:treatment>fix</PDBx:treatment>
<PDBx:value>1.00</PDBx:value>
</PDBx:refine_occupancy>
<PDBx:refine_occupancy class="solvent" pdbx_refine_id="X-ray">
<PDBx:details></PDBx:details>
<PDBx:treatment>fix</PDBx:treatment>
<PDBx:value>1.00</PDBx:value>
</PDBx:refine_occupancy>
<PDBx:refine_occupancy class="inhibitor orientation 1" pdbx_refine_id="X-ray">
<PDBx:details></PDBx:details>
<PDBx:treatment>fix</PDBx:treatment>
<PDBx:value>0.65</PDBx:value>
</PDBx:refine_occupancy>
<PDBx:refine_occupancy class="inhibitor orientation 2" pdbx_refine_id="X-ray">
<PDBx:details> The inhibitor binds to the enzyme in two alternative
conformations. The occupancy of each conformation was
adjusted so as to result in approximately equal mean
thermal factors for the atoms in each conformation.</PDBx:details>
<PDBx:treatment>fix</PDBx:treatment>
<PDBx:value>0.35</PDBx:value>
</PDBx:refine_occupancy>
</PDBx:refine_occupancyCategory>
0
1
0
1
0
1
1
1
refine_occupancyCategory
This property indicates that datablock
has a category element refine_occupancy.
refine_occupancyItem
Abstract Datatype property for refine_occupancy items.
reference_to_refine_occupancy
cross-reference to refine_occupancy
refine_occupancy.details
A description of special aspects of the occupancy refinement for
a class of atoms described in attribute class in category refine_occupancy.
The inhibitor binds to the enzyme in two
alternative conformations. The occupancy of
each conformation was adjusted so as to result
in approximately equal mean thermal factors
for the atoms in each conformation.
fix
ref
The treatment of occupancies for a class of atoms
described in attribute class in category refine_occupancy.
refine_occupancy.value
The value of occupancy assigned to a class of atoms defined in
attribute class in category refine_occupancy. Meaningful only for atoms with fixed
occupancy.
1.0
0.41
refine_occupancy.class
The class of atoms treated similarly for occupancy refinement.
all
protein
solvent
sugar-phosphate backbone
refine_occupancy.pdbx_refine_id
This data item uniquely identifies a refinement within an entry.
attribute pdbx_refine_id in category refine_occupancy can be used to distinguish the results
of joint refinements.
refln
Data items in the REFLN category record details about the
reflection data used to determine the ATOM_SITE data items.
The REFLN data items refer to individual reflections and must
be included in looped lists.
The REFLNS data items specify the parameters that apply to all
reflections. The REFLNS data items are not looped.
Example 1 - based on data set fetod of Todres, Yanovsky, Ermekov & Struchkov
[Acta Cryst. (1993), C49, 1352-1354].
<PDBx:reflnCategory>
<PDBx:refln index_h="2" index_k="0" index_l="0">
<PDBx:F_squared_calc>85.57</PDBx:F_squared_calc>
<PDBx:F_squared_meas>58.90</PDBx:F_squared_meas>
<PDBx:F_squared_sigma>1.45</PDBx:F_squared_sigma>
<PDBx:status>o</PDBx:status>
</PDBx:refln>
<PDBx:refln index_h="3" index_k="0" index_l="0">
<PDBx:F_squared_calc>15718.18</PDBx:F_squared_calc>
<PDBx:F_squared_meas>15631.06</PDBx:F_squared_meas>
<PDBx:F_squared_sigma>30.40</PDBx:F_squared_sigma>
<PDBx:status>o</PDBx:status>
</PDBx:refln>
<PDBx:refln index_h="4" index_k="0" index_l="0">
<PDBx:F_squared_calc>55613.11</PDBx:F_squared_calc>
<PDBx:F_squared_meas>49840.09</PDBx:F_squared_meas>
<PDBx:F_squared_sigma>61.86</PDBx:F_squared_sigma>
<PDBx:status>o</PDBx:status>
</PDBx:refln>
<PDBx:refln index_h="5" index_k="0" index_l="0">
<PDBx:F_squared_calc>246.85</PDBx:F_squared_calc>
<PDBx:F_squared_meas>241.86</PDBx:F_squared_meas>
<PDBx:F_squared_sigma>10.02</PDBx:F_squared_sigma>
<PDBx:status>o</PDBx:status>
</PDBx:refln>
<PDBx:refln index_h="6" index_k="0" index_l="0">
<PDBx:F_squared_calc>82.16</PDBx:F_squared_calc>
<PDBx:F_squared_meas>69.97</PDBx:F_squared_meas>
<PDBx:F_squared_sigma>1.93</PDBx:F_squared_sigma>
<PDBx:status>o</PDBx:status>
</PDBx:refln>
<PDBx:refln index_h="7" index_k="0" index_l="0">
<PDBx:F_squared_calc>1133.62</PDBx:F_squared_calc>
<PDBx:F_squared_meas>947.79</PDBx:F_squared_meas>
<PDBx:F_squared_sigma>11.78</PDBx:F_squared_sigma>
<PDBx:status>o</PDBx:status>
</PDBx:refln>
<PDBx:refln index_h="8" index_k="0" index_l="0">
<PDBx:F_squared_calc>2558.04</PDBx:F_squared_calc>
<PDBx:F_squared_meas>2453.33</PDBx:F_squared_meas>
<PDBx:F_squared_sigma>20.44</PDBx:F_squared_sigma>
<PDBx:status>o</PDBx:status>
</PDBx:refln>
<PDBx:refln index_h="9" index_k="0" index_l="0">
<PDBx:F_squared_calc>283.88</PDBx:F_squared_calc>
<PDBx:F_squared_meas>393.66</PDBx:F_squared_meas>
<PDBx:F_squared_sigma>7.79</PDBx:F_squared_sigma>
<PDBx:status>o</PDBx:status>
</PDBx:refln>
<PDBx:refln index_h="10" index_k="0" index_l="0">
<PDBx:F_squared_calc>283.70</PDBx:F_squared_calc>
<PDBx:F_squared_meas>171.98</PDBx:F_squared_meas>
<PDBx:F_squared_sigma>4.26</PDBx:F_squared_sigma>
<PDBx:status>o</PDBx:status>
</PDBx:refln>
</PDBx:reflnCategory>
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reflnCategory
This property indicates that datablock
has a category element refln.
reflnItem
Abstract Datatype property for refln items.
reference_to_refln
cross-reference to refln
refln.A_calc
The calculated value of structure-factor component A in
electrons.
A = |F|cos(phase)
refln.A_calc_au
The calculated value of structure-factor component A in
arbitrary units.
A = |F|cos(phase)
refln.A_meas
The measured value of structure-factor component A in electrons.
A = |F|cos(phase)
refln.A_meas_au
The measured value of structure-factor component A in
arbitrary units.
A = |F|cos(phase)
refln.B_calc
The calculated value of structure-factor component B in
electrons.
B = |F|sin(phase)
refln.B_calc_au
The calculated value of structure-factor component B in
arbitrary units.
B = |F|sin(phase)
refln.B_meas
The measured value of structure-factor component B in electrons.
B = |F|sin(phase)
refln.B_meas_au
The measured value of structure-factor component B in
arbitrary units.
B = |F|sin(phase)
refln.F_calc
The calculated value of the structure factor in electrons.
refln.F_calc_au
The calculated value of the structure factor in arbitrary
units.
refln.F_meas
The measured value of the structure factor in electrons.
refln.F_meas_au
The measured value of the structure factor in arbitrary units.
refln.F_meas_sigma
The standard uncertainty (estimated standard deviation) of
attribute F_meas in category refln in electrons.
refln.F_meas_sigma_au
The standard uncertainty (estimated standard deviation) of
attribute F_meas_au in category refln in arbitrary units.
refln.F_squared_calc
The calculated value of the squared structure factor in
electrons squared.
refln.F_squared_meas
The measured value of the squared structure factor in electrons
squared.
refln.F_squared_sigma
The standard uncertainty (derived from measurement) of the
squared structure factor in electrons squared.
refln.class_code
The code identifying the class to which this reflection has been
assigned. This code must match a value of attribute code.
in category reflns_class Reflections may be grouped into classes for a variety of
purposes. For example, for modulated structures each reflection
class may be defined by the number m=sum|m~i~|, where the m~i~
are the integer coefficients that, in addition to h,k,l, index
the corresponding diffraction vector in the basis defined
for the reciprocal lattice.
refln.crystal_id
This data item is a pointer to attribute id in category exptl_crystal in the
EXPTL_CRYSTAL category.
refln.d_spacing
The d spacing in angstroms for this reflection. This is related
to the (sin theta)/lambda value by the expression
attribute d_spacing in category refln = 2/(_refln.sint/lambda).
refln.fom
The figure of merit m for this reflection.
int P~alpha~ exp(i*alpha) dalpha
m = --------------------------------
int P~alpha~ dalpha
P~a~ = the probability that the phase angle a is correct
int is taken over the range alpha = 0 to 2 pi.
o
<
-
x
h
l
Classification of a reflection so as to indicate its status with
respect to inclusion in the refinement and the calculation of
R factors.
refln.intensity_calc
The calculated value of the intensity in the same units as
attribute intensity_meas in category refln.
refln.intensity_meas
The measured value of the intensity.
refln.intensity_sigma
The standard uncertainty (derived from measurement) of the
intensity in the same units as attribute intensity_meas in category refln.
refln.mean_path_length_tbar
Mean path length in millimetres through the crystal for this
reflection.
refln.pdbx_F_calc_part_solvent
The calculated value of the structure factor in arbitrary
units reflecting only the contribution of the solvent model.
refln.pdbx_F_calc_with_solvent
The calculated value of the structure factor in arbitrary
units including the contribution of the solvent model.
refln.pdbx_F_minus
The structure factor F(-h,-k,-l) of the Friedel pair.
refln.pdbx_F_minus_sigma
The standard uncertainty (derived from measurement) of the
structure factor F(-h,-k,-l) of the Friedel pair.
refln.pdbx_F_plus
The structure factor F(h,k,l) of the Friedel pair.
refln.pdbx_F_plus_sigma
The standard uncertainty (derived from measurement) of the
structure factor F(h,k,l) of the Friedel pair.
refln.pdbx_HL_A_iso
The isomorphous Hendrickson-Lattman coefficient A~iso~ for this
reflection.
Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta
Cryst. B26, 136-143.
refln.pdbx_HL_B_iso
The isomorphous Hendrickson-Lattman coefficient B~iso~ for this
reflection.
Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta
Cryst. B26, 136-143.
refln.pdbx_HL_C_iso
The isomorphous Hendrickson-Lattman coefficient C~iso~ for this
reflection.
Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta
Cryst. B26, 136-143.
refln.pdbx_HL_D_iso
The isomorphous Hendrickson-Lattman coefficient D~iso~ for this
reflection.
Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta
Cryst. B26, 136-143.
refln.pdbx_I_minus
The intensity of the I(-h,-k,-l) partner
of the Friedel pair.
refln.pdbx_I_minus_sigma
The standard uncertainty (derived from measurement) of the
intensity I(-h,-k,-l) partner of the Friedel pair.
refln.pdbx_I_plus
The intensity of the I(h,k,l) partner of
the Friedel pair.
refln.pdbx_I_plus_sigma
The standard uncertainty (derived from measurement) of the
intensity I(h,k,l) partner of the Friedel pair.
refln.pdbx_anom_difference
The amplitude difference of the Friedel pair,
D(hkl) = F(hkl) - F(-h-k-l).
refln.pdbx_anom_difference_sigma
The the standard deviation of the amplitude difference
of the Friedel pair, D(hkl) = F(hkl) - F(-h-k-l).
refln.pdbx_phase_calc_part_solvent
The calculated structure-factor phase in degrees reflecting
only the contribution of the solvent model.
refln.pdbx_phase_calc_with_solvent
The calculated structure-factor phase in degrees including
the contribution of the solvent model.
refln.phase_calc
The calculated structure-factor phase in degrees.
refln.phase_meas
The measured structure-factor phase in degrees.
incl
excl
extn
Status of a reflection in the structure-refinement process.
refln.scale_group_code
This data item is a pointer to attribute group_code in category reflns_scale in the
REFLNS_SCALE category.
refln.sint_over_lambda
The (sin theta)/lambda value in reciprocal angstroms for this
reflection.
o
<
-
x
h
l
f
Classification of a reflection so as to indicate its status with
respect to inclusion in the refinement and the calculation of
R factors.
refln.symmetry_epsilon
The symmetry reinforcement factor corresponding to the number of
times the reflection indices are generated identically from the
space-group symmetry operations.
refln.symmetry_multiplicity
The number of symmetry-equivalent reflections. The equivalent
reflections have the same structure-factor magnitudes because
of the space-group symmetry and the Friedel relationship.
refln.wavelength
The mean wavelength in angstroms of radiation used to measure
this reflection. This is an important parameter for data
collected using energy-dispersive detectors or the Laue
method.
refln.wavelength_id
This data item is a pointer to attribute wavelength_id in category diffrn_radiation in
the DIFFRN_RADIATION category.
refln.index_h
Miller index h of the reflection. The values of the Miller
indices in the REFLN category must correspond to the cell
defined by cell lengths and cell angles in the CELL category.
refln.index_k
Miller index k of the reflection. The values of the Miller
indices in the REFLN category must correspond to the cell
defined by cell lengths and cell angles in the CELL category.
refln.index_l
Miller index l of the reflection. The values of the Miller
indices in the REFLN category must correspond to the cell
defined by cell lengths and cell angles in the CELL category.
refln_sys_abs
Data items in the REFLN_SYS_ABS category record details about
the reflection data that should be systematically absent,
given the designated space group.
Example 1 - hypothetical example.
<PDBx:refln_sys_absCategory>
<PDBx:refln_sys_abs index_h="0" index_k="3" index_l="0">
<PDBx:I>28.32</PDBx:I>
<PDBx:I_over_sigmaI>1.23</PDBx:I_over_sigmaI>
<PDBx:sigmaI>22.95</PDBx:sigmaI>
</PDBx:refln_sys_abs>
<PDBx:refln_sys_abs index_h="0" index_k="5" index_l="0">
<PDBx:I>14.11</PDBx:I>
<PDBx:I_over_sigmaI>0.86</PDBx:I_over_sigmaI>
<PDBx:sigmaI>16.38</PDBx:sigmaI>
</PDBx:refln_sys_abs>
<PDBx:refln_sys_abs index_h="0" index_k="7" index_l="0">
<PDBx:I>114.81</PDBx:I>
<PDBx:I_over_sigmaI>5.67</PDBx:I_over_sigmaI>
<PDBx:sigmaI>20.22</PDBx:sigmaI>
</PDBx:refln_sys_abs>
<PDBx:refln_sys_abs index_h="0" index_k="9" index_l="0">
<PDBx:I>32.99</PDBx:I>
<PDBx:I_over_sigmaI>1.35</PDBx:I_over_sigmaI>
<PDBx:sigmaI>24.51</PDBx:sigmaI>
</PDBx:refln_sys_abs>
</PDBx:refln_sys_absCategory>
0
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refln_sys_absCategory
This property indicates that datablock
has a category element refln_sys_abs.
refln_sys_absItem
Abstract Datatype property for refln_sys_abs items.
reference_to_refln_sys_abs
cross-reference to refln_sys_abs
refln_sys_abs.I
The measured value of the intensity in arbitrary units.
refln_sys_abs.I_over_sigmaI
The ratio of _refln_sys_abs.I to _refln_sys_abs.sigmaI. Used
to evaluate whether a reflection that should be systematically
absent according to the designated space group is in fact
absent.
refln_sys_abs.sigmaI
The standard uncertainty (estimated standard deviation) of
attribute I in category refln_sys_abs in arbitrary units.
refln_sys_abs.index_h
Miller index h of the reflection. The values of the Miller
indices in the REFLN_SYS_ABS category must correspond to
the cell defined by cell lengths and cell angles in the CELL
category.
refln_sys_abs.index_k
Miller index k of the reflection. The values of the Miller
indices in the REFLN_SYS_ABS category must correspond to the
cell defined by cell lengths and cell angles in the CELL
category.
refln_sys_abs.index_l
Miller index l of the reflection. The values of the Miller
indices in the REFLN_SYS_ABS category must correspond to the
cell defined by cell lengths and cell angles in the CELL
category.
reflns
Data items in the REFLNS category record details about the
reflection data used to determine the ATOM_SITE data items.
The REFLN data items refer to individual reflections and must
be included in looped lists.
The REFLNS data items specify the parameters that apply to all
reflections. The REFLNS data items are not looped.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:reflnsCategory>
<PDBx:reflns entry_id="5HVP">
<PDBx:d_resolution_high>2.00</PDBx:d_resolution_high>
<PDBx:d_resolution_low>8.00</PDBx:d_resolution_low>
<PDBx:data_reduction_details> Merging and scaling based on only those reflections
with I > \s(I).</PDBx:data_reduction_details>
<PDBx:data_reduction_method> Xengen program scalei. Anomalous pairs were merged. Scaling
proceeded in several passes, beginning with 1-parameter
fit and ending with 3-parameter fit.</PDBx:data_reduction_method>
<PDBx:details>none</PDBx:details>
<PDBx:limit_h_max>22</PDBx:limit_h_max>
<PDBx:limit_h_min>0</PDBx:limit_h_min>
<PDBx:limit_k_max>46</PDBx:limit_k_max>
<PDBx:limit_k_min>0</PDBx:limit_k_min>
<PDBx:limit_l_max>57</PDBx:limit_l_max>
<PDBx:limit_l_min>0</PDBx:limit_l_min>
<PDBx:number_obs>7228</PDBx:number_obs>
<PDBx:observed_criterion>> 1 \s(I)</PDBx:observed_criterion>
</PDBx:reflns>
</PDBx:reflnsCategory>
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<PDBx:reflnsCategory>
<PDBx:reflns entry_id="1TOZ">
<PDBx:d_resolution_high>0.8733</PDBx:d_resolution_high>
<PDBx:d_resolution_low>11.9202</PDBx:d_resolution_low>
<PDBx:limit_h_max>6</PDBx:limit_h_max>
<PDBx:limit_h_min>0</PDBx:limit_h_min>
<PDBx:limit_k_max>17</PDBx:limit_k_max>
<PDBx:limit_k_min>0</PDBx:limit_k_min>
<PDBx:limit_l_max>22</PDBx:limit_l_max>
<PDBx:limit_l_min>0</PDBx:limit_l_min>
<PDBx:number_all>1592</PDBx:number_all>
<PDBx:number_obs>1408</PDBx:number_obs>
<PDBx:observed_criterion>F_>_6.0_\s(F)</PDBx:observed_criterion>
</PDBx:reflns>
</PDBx:reflnsCategory>
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reflnsCategory
This property indicates that datablock
has a category element reflns.
reflnsItem
Abstract Datatype property for reflns items.
reference_to_reflns
cross-reference to reflns
reflns.B_iso_Wilson_estimate
The value of the overall isotropic displacement parameter
estimated from the slope of the Wilson plot.
reflns.Friedel_coverage
The proportion of Friedel-related reflections present in
the number of 'independent' reflections specified by
the item attribute number_all.
in category reflns
This proportion is calculated as the ratio:
[N(Crystal class) - N(Laue symmetry)] / N(Laue symmetry)
where, working from the DIFFRN_REFLN list,
N(Crystal class) is the number of reflections obtained on
averaging under the symmetry of the crystal class
N(Laue symmetry) is the number of reflections obtained on
averaging under the Laue symmetry.
Examples:
(a) For centrosymmetric structures, the value of
attribute Friedel_coverage in category reflns is
necessarily equal to 0.0, as the crystal class
is identical to the Laue symmetry.
(b) For whole-sphere data for a crystal in the space
group P1, attribute Friedel_coverage in category reflns is equal to 1.0,
as no reflection h k l is equivalent to -h -k -l
in the crystal class and all Friedel pairs
{h k l; -h -k -l} have been measured.
(c) For whole-sphere data in space group Pmm2,
attribute Friedel_coverage
in category reflns will be < 1.0 because although reflections h k l and
-h -k -l are not equivalent when h k l indices are
nonzero, they are when l=0.
(d) For a crystal in space group Pmm2, measurements of the
two inequivalent octants h >= 0, k >=0, l lead to the
same value as in (c), whereas measurements of the
two equivalent octants h >= 0, k, l >= 0 will lead to
a zero value for attribute Friedel_coverage in category reflns.
reflns.R_free_details
A description of the method by which a subset of reflections was
selected for exclusion from refinement so as to be used in the
calculation of a 'free' R factor.
The data set was sorted with l varying most
rapidly and h varying least rapidly. Every
10th reflection in this sorted list was
excluded from refinement and included in the
calculation of a 'free' R factor.
reflns.Rmerge_F_all
Residual factor Rmerge for all reflections that satisfy the
resolution limits established by attribute d_resolution_high
in category reflns and attribute d_resolution_low.
in category reflns
sum~i~(sum~j~|F~j~ - <F>|)
Rmerge(F) = --------------------------
sum~i~(sum~j~<F>)
F~j~ = the amplitude of the jth observation of reflection i
<F> = the mean of the amplitudes of all observations of
reflection i
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection
reflns.Rmerge_F_obs
Residual factor Rmerge for reflections that satisfy the
resolution limits established by attribute d_resolution_high
in category reflns and attribute d_resolution_low in category reflns and the observation limit
established by attribute observed_criterion.
in category reflns
sum~i~(sum~j~|F~j~ - <F>|)
Rmerge(F) = --------------------------
sum~i~(sum~j~<F>)
F~j~ = the amplitude of the jth observation of reflection i
<F> = the mean of the amplitudes of all observations of
reflection i
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection
reflns.d_resolution_high
The smallest value for the interplanar spacings for
the reflection data. This is called the highest resolution.
reflns.d_resolution_low
The largest value for the interplanar spacings for the
reflection data. This is called the lowest resolution.
reflns.data_reduction_details
A description of special aspects of the data-reduction
procedures.
Merging and scaling based on only those
reflections with I > sig(I).
reflns.data_reduction_method
The method used for data reduction.
Note that this is not the computer program used, which is
described in the SOFTWARE category, but the method
itself.
This data item should be used to describe significant
methodological options used within the data-reduction programs.
Profile fitting by method of Kabsch (1987).
Scaling used spherical harmonic coefficients.
reflns.details
A description of reflection data not covered by other data
names. This should include details of the Friedel pairs.
reflns.limit_h_max
Maximum value of the Miller index h for the reflection data. This
need not have the same value as attribute limit_h_max in category diffrn_reflns.
reflns.limit_h_min
Minimum value of the Miller index h for the reflection data. This
need not have the same value as attribute limit_h_min in category diffrn_reflns.
reflns.limit_k_max
Maximum value of the Miller index k for the reflection data. This
need not have the same value as attribute limit_k_max in category diffrn_reflns.
reflns.limit_k_min
Minimum value of the Miller index k for the reflection data. This
need not have the same value as attribute limit_k_min in category diffrn_reflns.
reflns.limit_l_max
Maximum value of the Miller index l for the reflection data. This
need not have the same value as attribute limit_l_max in category diffrn_reflns.
reflns.limit_l_min
Minimum value of the Miller index l for the reflection data. This
need not have the same value as attribute limit_l_min in category diffrn_reflns.
reflns.number_all
The total number of reflections in the REFLN list (not the
DIFFRN_REFLN list). This number may contain Friedel-equivalent
reflections according to the nature of the structure and the
procedures used. The item attribute details in category reflns describes the
reflection data.
reflns.number_gt
The number of reflections in the REFLN list (not the
DIFFRN_REFLN list) that are significantly intense, satisfying
the criterion specified by attribute threshold_expression in category reflns. This may
include Friedel-equivalent reflections (i.e. those which are
symmetry-equivalent under the Laue symmetry but inequivalent
under the crystal class) according to the nature of the
structure and the procedures used. Any special characteristics
of the reflections included in the REFLN list should be
described using the item attribute details in category reflns.
reflns.number_obs
The number of reflections in the REFLN list (not the DIFFRN_REFLN
list) classified as observed (see attribute observed_criterion).
in category reflns This number may contain Friedel-equivalent reflections according
to the nature of the structure and the procedures used.
reflns.observed_criterion
The criterion used to classify a reflection as 'observed'. This
criterion is usually expressed in terms of a sigma(I) or
sigma(F) threshold.
>2sigma(I)
reflns.observed_criterion_F_max
The criterion used to classify a reflection as 'observed'
expressed as an upper limit for the value of F.
reflns.observed_criterion_F_min
The criterion used to classify a reflection as 'observed'
expressed as a lower limit for the value of F.
reflns.observed_criterion_I_max
The criterion used to classify a reflection as 'observed'
expressed as an upper limit for the value of I.
reflns.observed_criterion_I_min
The criterion used to classify a reflection as 'observed'
expressed as a lower limit for the value of I.
reflns.observed_criterion_sigma_F
The criterion used to classify a reflection as 'observed'
expressed as a multiple of the value of sigma(F).
reflns.observed_criterion_sigma_I
The criterion used to classify a reflection as 'observed'
expressed as a multiple of the value of sigma(I).
reflns.pdbx_Rmerge_I_all
The R value for merging all intensities in this data set.
reflns.pdbx_Rmerge_I_obs
The R value for merging intensities satisfying the observed
criteria in this data set.
reflns.pdbx_Rpim_I_all
The precision-indicating merging R factor value Rpim,
for merging all intensities in this data set.
sum~i~ [1/(N~i~ - 1)]1/2^ sum~j~ | I~j~ - <I~i~> |
Rpim = --------------------------------------------------
sum~i~ ( sum~j~ I~j~ )
I~j~ = the intensity of the jth observation of reflection i
<I~i~> = the mean of the intensities of all observations
of reflection i
N~i~ = the redundancy (the number of times reflection i
has been measured).
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection.
Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct.
Biol. 4, 269-275.
Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst.
30, 203-205.
Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135.
reflns.pdbx_Rrim_I_all
The redundancy-independent merging R factor value Rrim,
also denoted Rmeas, for merging all intensities in this
data set.
sum~i~ [N~i~/(N~i~ - 1)]1/2^ sum~j~ | I~j~ - <I~i~> |
Rrim = ----------------------------------------------------
sum~i~ ( sum~j~ I~j~ )
I~j~ = the intensity of the jth observation of reflection i
<I~i~> = the mean of the intensities of all observations of
reflection i
N~i~ = the redundancy (the number of times reflection i
has been measured).
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection.
Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct.
Biol. 4, 269-275.
Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst.
30, 203-205.
Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135.
reflns.pdbx_Rsym_value
R Sym value in percent.
2.0
reflns.pdbx_chi_squared
Overall Chi-squared statistic.
reflns.pdbx_d_opt
The optical resolution of the data set, d(opt), is the
expected minimum distance between two resolved peaks in
an electron-density map.
d(opt) = {2[sigma(Patt)2^ + sigma(sph)2^]}1/2^
sigma(Patt) = standard deviation of the Gaussian function
fitted to the Patterson origin peak
sigma(sph) = standard deviation of the Gaussian function
fitted to the origin peak of the spherical
interference function, representing the Fourier
transform of a sphere with radius 1/dmin
dmin = nominal resolution (_reflns.d_resolution_high)
Ref: Vaguine, A. A., Richelle, J. & Wodak, S. J. (1999).
Acta Cryst. D55, 191-205.
(see also http://www.ysbl.york.ac.uk/~alexei/sfcheck.html)
Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135.
reflns.pdbx_d_res_high_opt
The highest optical resolution for this reflection data set
as determined by computational method attribute pdbx_d_res_opt_method in category reflns.
1.2
reflns.pdbx_d_res_low_opt
The lowest optical resolution for this reflection data set
as determined by computational method attribute pdbx_d_res_opt_method in category reflns.
20.5
reflns.pdbx_d_res_opt_method
The computational method used to determine the optical
resolution limits attribute pdbx_d_res_high_opt in category reflns and
attribute pdbx_d_res_low_opt in category reflns.
SFCHECK
reflns.pdbx_netI_over_av_sigmaI
The ratio of the average intensity to the average uncertainty,
<I>/<sigma(I)>.
reflns.pdbx_netI_over_sigmaI
The mean of the ratio of the intensities to their
standard uncertainties, <I/sigma(I)>.
reflns.pdbx_number_measured_all
Total number of measured reflections.
23000
140000
reflns.pdbx_redundancy
Overall redundancy for this data set (%).
reflns.pdbx_res_netI_over_av_sigmaI_2
Resolution (angstrom) for reflections with <I>/<sigma(I)> = 2.
reflns.pdbx_res_netI_over_sigmaI_2
Resolution (angstroms) for reflections with <I/sigma(I)> = 2.
reflns.pdbx_scaling_rejects
Number of reflections rejected in scaling operations.
reflns.percent_possible_obs
The percentage of geometrically possible reflections represented
by reflections that satisfy the resolution limits established
by _reflns.d_resolution_high and _reflns.d_resolution_low and
the observation limit established by
attribute observed_criterion in category reflns.
reflns.threshold_expression
The threshold, usually based on multiples of u(I), u(F^2^)
or u(F), that serves to identify significantly intense
reflections, the number of which is given by attribute number_gt.
in category reflns These reflections are used in the calculation of
attribute ls_R_factor_gt in category refine.
I>2u(I)
reflns.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
reflns_class
Data items in the REFLNS_CLASS category record details
of the reflections used to determine the structural
parameters for each reflection class.
Example 1 - example corresponding to the one-dimensional incommensurately
modulated structure of K~2~SeO~4~.
<PDBx:reflns_classCategory>
<PDBx:reflns_class code="Main">
<PDBx:number_gt>584</PDBx:number_gt>
</PDBx:reflns_class>
<PDBx:reflns_class code="Sat1">
<PDBx:number_gt>226</PDBx:number_gt>
</PDBx:reflns_class>
<PDBx:reflns_class code="Sat2">
<PDBx:number_gt>50</PDBx:number_gt>
</PDBx:reflns_class>
</PDBx:reflns_classCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
reflns_classCategory
This property indicates that datablock
has a category element reflns_class.
reflns_classItem
Abstract Datatype property for reflns_class items.
reference_to_reflns_class
cross-reference to reflns_class
reflns_class.R_Fsqd_factor
For each reflection class, the residual factor R(F^2^) calculated
on the squared amplitudes of the observed and calculated
structure factors for the reflections judged significantly
intense (i.e. satisfying the threshold specified by
attribute threshold_expression) in category reflns and included in the refinement.
The reflections also satisfy the resolution limits established
by _reflns_class.d_res_high and _reflns_class.d_res_low.
sum | F(obs)^2^ - F(calc)^2^ |
R(Fsqd) = -------------------------------
sum F(obs)^2^
F(obs)^2^ = squares of the observed structure-factor amplitudes
F(calc)^2^ = squares of the calculated structure-factor
amplitudes
and the sum is taken over the reflections of this class.
reflns_class.R_I_factor
For each reflection class, the residual factor R(I) for the
reflections judged significantly intense (i.e. satisfying the
threshold specified by attribute threshold_expression) in category reflns and
included in the refinement.
This is most often calculated in Rietveld refinements
against powder data, where it is referred to as R~B~ or R~Bragg~.
sum | I(obs) - I(calc) |
R(I) = ------------------------
sum | I(obs) |
I(obs) = the net observed intensities
I(calc) = the net calculated intensities
and the sum is taken over the reflections of this class.
reflns_class.R_factor_all
For each reflection class, the residual factor for all
reflections included in the refinement.
The reflections also satisfy the resolution limits established by
_reflns_class.d_res_high and _reflns_class.d_res_low.
This is the conventional R factor. See also the
definition of attribute wR_factor_all.
in category reflns_class
sum | F(obs) - F(calc) |
R = ------------------------
sum | F(obs) |
F(obs) = the observed structure-factor amplitudes
F(calc) = the calculated structure-factor amplitudes
and the sum is taken over the reflections of this class.
reflns_class.R_factor_gt
For each reflection class, the residual factor for significantly
intense reflections (see attribute threshold_expression) in category reflns included
in the refinement.
The reflections also satisfy the resolution limits established by
_reflns_class.d_res_high and _reflns_class.d_res_low.
This is the conventional R factor. See also the
definition of attribute wR_factor_all.
in category reflns_class
sum | F(obs) - F(calc) |
R = ------------------------
sum | F(obs) |
F(obs) = the observed structure-factor amplitudes
F(calc) = the calculated structure-factor amplitudes
and the sum is taken over the reflections of this class.
reflns_class.d_res_high
For each reflection class, the smallest value in angstroms
for the interplanar spacings for the reflections used in the
refinement. This is called the highest resolution.
reflns_class.d_res_low
For each reflection class, the largest value in angstroms
for the interplanar spacings for the reflections used in the
refinement. This is called the lowest resolution.
reflns_class.description
Description of each reflection class.
m=1 first order satellites
H0L0 common projection reflections
reflns_class.number_gt
For each reflection class, the number of significantly intense
reflections (see attribute threshold_expression) in category reflns in the REFLN
list (not the DIFFRN_REFLN list). This may include Friedel-
equivalent reflections (i.e. those which are symmetry-equivalent
under the Laue symmetry but inequivalent under the crystal
class) according to the nature of the structure and the
procedures used. Any special characteristics of the reflections
included in the REFLN list should be described using the item
attribute details in category reflns.
reflns_class.number_total
For each reflection class, the total number of reflections
in the REFLN list (not the DIFFRN_REFLN list). This may
include Friedel-equivalent reflections (i.e. those which are
symmetry-equivalent under the Laue symmetry but inequivalent
under the crystal class) according to the nature of the
structure and the procedures used. Any special characteristics
of the reflections included in the REFLN list should be
described using the item attribute details in category reflns.
reflns_class.wR_factor_all
For each reflection class, the weighted residual factors for all
reflections included in the refinement. The reflections also
satisfy the resolution limits established by
_reflns_class.d_res_high and _reflns_class.d_res_low.
See also attribute R_factor_ in category reflns_class definitions.
( sum w [ Y(obs) - Y(calc) ]^2^ )^1/2^
wR = ( ------------------------------ )
( sum w Y(obs)^2^ )
Y(obs) = the observed amplitude specified by
attribute ls_structure_factor_coef
in category refine Y(calc) = the calculated amplitude specified by
attribute ls_structure_factor_coef
in category refine w = the least-squares weight
and the sum is taken over the reflections of this class.
reflns_class.code
The code identifying a certain reflection class.
1
m1
s2
reflns_scale
Data items in the REFLNS_SCALE category record details about
the structure-factor scales. They are referenced from within
the REFLN list through attribute scale_group_code in category refln.
Example 1 - based on laboratory records for the collagen-like
peptide [(POG)4 EKG (POG)5]3.
<PDBx:reflns_scaleCategory>
<PDBx:reflns_scale group_code="SG1">
<PDBx:meas_F>4.0</PDBx:meas_F>
</PDBx:reflns_scale>
</PDBx:reflns_scaleCategory>
0
1
0
1
0
1
1
reflns_scaleCategory
This property indicates that datablock
has a category element reflns_scale.
reflns_scaleItem
Abstract Datatype property for reflns_scale items.
reference_to_reflns_scale
cross-reference to reflns_scale
reflns_scale.meas_F
A scale associated with attribute group_code in category reflns_scale.
reflns_scale.meas_F_squared
A scale associated with attribute group_code in category reflns_scale.
reflns_scale.meas_intensity
A scale associated with attribute group_code in category reflns_scale.
reflns_scale.group_code
The code identifying a scale attribute meas_F,
in category reflns_scale _reflns_scale.meas_F_squared or _reflns_scale.meas_intensity.
These are linked to the REFLN list by the
attribute scale_group_code in category refln. These codes
need not correspond to those in the DIFFRN_SCALE list.
1
2
c1
c2
reflns_shell
Data items in the REFLNS_SHELL category record details about
the reflection data used to determine the ATOM_SITE data items
broken down into shells of resolution.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:reflns_shellCategory>
<PDBx:reflns_shell d_res_high="31.38">
<PDBx:Rmerge_F_obs>1.98</PDBx:Rmerge_F_obs>
<PDBx:d_res_low>3.82</PDBx:d_res_low>
<PDBx:meanI_over_sigI_obs>69.8</PDBx:meanI_over_sigI_obs>
<PDBx:number_measured_obs>9024</PDBx:number_measured_obs>
<PDBx:number_unique_obs>2540</PDBx:number_unique_obs>
<PDBx:percent_possible_obs>96.8</PDBx:percent_possible_obs>
</PDBx:reflns_shell>
<PDBx:reflns_shell d_res_high="3.82">
<PDBx:Rmerge_F_obs>3.85</PDBx:Rmerge_F_obs>
<PDBx:d_res_low>3.03</PDBx:d_res_low>
<PDBx:meanI_over_sigI_obs>26.1</PDBx:meanI_over_sigI_obs>
<PDBx:number_measured_obs>7413</PDBx:number_measured_obs>
<PDBx:number_unique_obs>2364</PDBx:number_unique_obs>
<PDBx:percent_possible_obs>95.1</PDBx:percent_possible_obs>
</PDBx:reflns_shell>
<PDBx:reflns_shell d_res_high="3.03">
<PDBx:Rmerge_F_obs>6.37</PDBx:Rmerge_F_obs>
<PDBx:d_res_low>2.65</PDBx:d_res_low>
<PDBx:meanI_over_sigI_obs>10.5</PDBx:meanI_over_sigI_obs>
<PDBx:number_measured_obs>5640</PDBx:number_measured_obs>
<PDBx:number_unique_obs>2123</PDBx:number_unique_obs>
<PDBx:percent_possible_obs>86.2</PDBx:percent_possible_obs>
</PDBx:reflns_shell>
<PDBx:reflns_shell d_res_high="2.65">
<PDBx:Rmerge_F_obs>8.01</PDBx:Rmerge_F_obs>
<PDBx:d_res_low>2.41</PDBx:d_res_low>
<PDBx:meanI_over_sigI_obs>6.4</PDBx:meanI_over_sigI_obs>
<PDBx:number_measured_obs>4322</PDBx:number_measured_obs>
<PDBx:number_unique_obs>1882</PDBx:number_unique_obs>
<PDBx:percent_possible_obs>76.8</PDBx:percent_possible_obs>
</PDBx:reflns_shell>
<PDBx:reflns_shell d_res_high="2.41">
<PDBx:Rmerge_F_obs>9.86</PDBx:Rmerge_F_obs>
<PDBx:d_res_low>2.23</PDBx:d_res_low>
<PDBx:meanI_over_sigI_obs>4.3</PDBx:meanI_over_sigI_obs>
<PDBx:number_measured_obs>3247</PDBx:number_measured_obs>
<PDBx:number_unique_obs>1714</PDBx:number_unique_obs>
<PDBx:percent_possible_obs>70.4</PDBx:percent_possible_obs>
</PDBx:reflns_shell>
<PDBx:reflns_shell d_res_high="2.23">
<PDBx:Rmerge_F_obs>13.99</PDBx:Rmerge_F_obs>
<PDBx:d_res_low>2.10</PDBx:d_res_low>
<PDBx:meanI_over_sigI_obs>3.1</PDBx:meanI_over_sigI_obs>
<PDBx:number_measured_obs>1140</PDBx:number_measured_obs>
<PDBx:number_unique_obs>812</PDBx:number_unique_obs>
<PDBx:percent_possible_obs>33.3</PDBx:percent_possible_obs>
</PDBx:reflns_shell>
</PDBx:reflns_shellCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
reflns_shellCategory
This property indicates that datablock
has a category element reflns_shell.
reflns_shellItem
Abstract Datatype property for reflns_shell items.
reference_to_reflns_shell
cross-reference to reflns_shell
reflns_shell.Rmerge_F_all
Residual factor Rmerge for all reflections that satisfy the
resolution limits established by attribute d_res_high in category reflns_shell and
attribute d_res_low.
in category reflns_shell
sum~i~(sum~j~|F~j~ - <F>|)
Rmerge(F) = --------------------------
sum~i~(sum~j~<F>)
F~j~ = the amplitude of the jth observation of reflection i
<F> = the mean of the amplitudes of all observations of
reflection i
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection
reflns_shell.Rmerge_F_gt
The value of Rmerge(F) for significantly intense reflections
(see attribute threshold_expression) in category reflns in a given shell.
sum~i~ ( sum~j~ | F~j~ - <F> | )
Rmerge(F) = --------------------------------
sum~i~ ( sum~j~ <F> )
F~j~ = the amplitude of the jth observation of reflection i
<F> = the mean of the amplitudes of all observations of
reflection i
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection.
reflns_shell.Rmerge_F_obs
Residual factor Rmerge for reflections that satisfy the
resolution limits established by attribute d_res_high in category reflns_shell and
attribute d_res_low in category reflns_shell and the observation criterion
established by attribute observed_criterion.
in category reflns
sum~i~(sum~j~|F~j~ - <F>|)
Rmerge(F) = --------------------------
sum~i~(sum~j~<F>)
F~j~ = the amplitude of the jth observation of reflection i
<F> = the mean of the amplitudes of all observations of
reflection i
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection
reflns_shell.Rmerge_I_all
The value of Rmerge(I) for all reflections in a given shell.
sum~i~(sum~j~|I~j~ - <I>|)
Rmerge(I) = --------------------------
sum~i~(sum~j~<I>)
I~j~ = the intensity of the jth observation of reflection i
<I> = the mean of the intensities of all observations of
reflection i
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection
reflns_shell.Rmerge_I_gt
The value of Rmerge(I) for significantly intense reflections
(see attribute threshold_expression) in category reflns in a given shell.
sum~i~ ( sum~j~ | I~j~ - <I> | )
Rmerge(I) = --------------------------------
sum~i~ ( sum~j~ <I> )
I~j~ = the intensity of the jth observation of reflection i
<I> = the mean of the intensities of all observations of
reflection i
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection.
reflns_shell.Rmerge_I_obs
The value of Rmerge(I) for reflections classified as 'observed'
(see attribute observed_criterion) in category reflns in a given shell.
sum~i~(sum~j~|I~j~ - <I>|)
Rmerge(I) = --------------------------
sum~i~(sum~j~<I>)
I~j~ = the intensity of the jth observation of reflection i
<I> = the mean of the intensities of all observations of
reflection i
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection
reflns_shell.d_res_low
The highest value in angstroms for the interplanar spacings
for the reflections in this shell. This is called the lowest
resolution.
reflns_shell.meanI_over_sigI_all
The ratio of the mean of the intensities of all reflections
in this shell to the mean of the standard uncertainties of the
intensities of all reflections in this shell.
reflns_shell.meanI_over_sigI_gt
The ratio of the mean of the intensities of the significantly
intense reflections (see attribute threshold_expression) in category reflns in
this shell to the mean of the standard uncertainties of the
intensities of the significantly intense reflections in this
shell.
reflns_shell.meanI_over_sigI_obs
The ratio of the mean of the intensities of the reflections
classified as 'observed' (see attribute observed_criterion) in category reflns in
this shell to the mean of the standard uncertainties of the
intensities of the 'observed' reflections in this
shell.
reflns_shell.meanI_over_uI_all
The ratio of the mean of the intensities of all reflections
in this shell to the mean of the standard uncertainties of the
intensities of all reflections in this shell.
reflns_shell.meanI_over_uI_gt
The ratio of the mean of the intensities of the significantly
intense reflections (see attribute threshold_expression) in category reflns in
this shell to the mean of the standard uncertainties of the
intensities of the significantly intense reflections in this
shell.
reflns_shell.number_measured_all
The total number of reflections measured for this
shell.
reflns_shell.number_measured_gt
The number of significantly intense reflections
(see attribute threshold_expression) in category reflns measured for this
shell.
reflns_shell.number_measured_obs
The number of reflections classified as 'observed'
(see attribute observed_criterion) in category reflns for this
shell.
reflns_shell.number_possible
The number of unique reflections it is possible to measure in
this shell.
reflns_shell.number_unique_all
The total number of measured reflections which are symmetry-
unique after merging for this shell.
reflns_shell.number_unique_gt
The total number of significantly intense reflections
(see attribute threshold_expression) in category reflns resulting from merging
measured symmetry-equivalent reflections for this resolution
shell.
reflns_shell.number_unique_obs
The total number of measured reflections classified as 'observed'
(see attribute observed_criterion) in category reflns which are symmetry-unique
after merging for this shell.
reflns_shell.pdbx_Rpim_I_all
The precision-indicating merging R factor value Rpim,
for merging all intensities in a given shell.
sum~i~ [1/(N~i~ - 1)]1/2^ sum~j~ | I~j~ - <I~i~> |
Rpim = --------------------------------------------------
sum~i~ ( sum~j~ I~j~ )
I~j~ = the intensity of the jth observation of reflection i
<I~i~> = the mean of the intensities of all observations of
reflection i
N~i~ = the redundancy (the number of times reflection i
has been measured).
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection.
Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct.
Biol. 4, 269-275.
Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst.
30, 203-205.
Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135.
reflns_shell.pdbx_Rrim_I_all
The redundancy-independent merging R factor value Rrim,
also denoted Rmeas, for merging all intensities in a
given shell.
sum~i~ [N~i~ /( N~i~ - 1)]1/2^ sum~j~ | I~j~ - <I~i~> |
Rrim = --------------------------------------------------------
sum~i~ ( sum~j~ I~j~ )
I~j~ = the intensity of the jth observation of reflection i
<I~i~> = the mean of the intensities of all observations of
reflection i
N~i~ = the redundancy (the number of times reflection i
has been measured).
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection.
Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct.
Biol. 4, 269-275.
Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst.
30, 203-205.
Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135.
reflns_shell.pdbx_Rsym_value
R sym value in percent.
reflns_shell.pdbx_chi_squared
Chi-squared statistic for this resolution shell.
reflns_shell.pdbx_netI_over_sigmaI_all
The mean of the ratio of the intensities to their
standard uncertainties of all reflections in the
resolution shell.
attribute pdbx_netI_over_sigmaI_all in category reflns_shell = <I/sigma(I)>
reflns_shell.pdbx_netI_over_sigmaI_obs
The mean of the ratio of the intensities to their
standard uncertainties of observed reflections
(see attribute observed_criterion) in category reflns in the resolution shell.
attribute pdbx_netI_over_sigmaI_obs in category reflns_shell = <I/sigma(I)>
reflns_shell.pdbx_redundancy
Redundancy for the current shell.
reflns_shell.pdbx_rejects
The number of rejected reflections in the resolution
shell. Reflections may be rejected from scaling
by setting the observation criterion,
attribute observed_criterion.
in category reflns
reflns_shell.percent_possible_all
The percentage of geometrically possible reflections represented
by all reflections measured for this shell.
reflns_shell.percent_possible_gt
The percentage of geometrically possible reflections
represented by significantly intense reflections
(see attribute threshold_expression) in category reflns measured for this
shell.
reflns_shell.percent_possible_obs
The percentage of geometrically possible reflections represented
by reflections classified as 'observed' (see
attribute observed_criterion) in category reflns for this shell.
reflns_shell.d_res_high
The smallest value in angstroms for the interplanar spacings
for the reflections in this shell. This is called the highest
resolution.
software
Data items in the SOFTWARE category record details about
the software used in the structure analysis, which implies
any software used in the generation of any data items
associated with the structure determination and
structure representation.
These data items allow computer programs to be referenced
in more detail than data items in the COMPUTING category do.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:softwareCategory>
<PDBx:software pdbx_ordinal="1">
<PDBx:citation_id>ref5</PDBx:citation_id>
<PDBx:classification>refinement</PDBx:classification>
<PDBx:compiler_name>Convex Fortran</PDBx:compiler_name>
<PDBx:compiler_version>v8.0</PDBx:compiler_version>
<PDBx:contact_author>Wayne A. Hendrickson</PDBx:contact_author>
<PDBx:contact_author_email xsi:nil="true" />
<PDBx:date></PDBx:date>
<PDBx:dependencies>Requires that Protin be run first</PDBx:dependencies>
<PDBx:description>restrained least-squares refinement</PDBx:description>
<PDBx:hardware>Convex C220</PDBx:hardware>
<PDBx:language>Fortran</PDBx:language>
<PDBx:location>ftp://rosebud.sdsc.edu/pub/sdsc/xtal/CCP4/ccp4/</PDBx:location>
<PDBx:mods>optimized</PDBx:mods>
<PDBx:name>Prolsq</PDBx:name>
<PDBx:os>ConvexOS</PDBx:os>
<PDBx:os_version>v10.1</PDBx:os_version>
<PDBx:type>program</PDBx:type>
<PDBx:version>unknown</PDBx:version>
</PDBx:software>
</PDBx:softwareCategory>
0
1
1
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
0
1
0
1
0
1
0
1
1
softwareCategory
This property indicates that datablock
has a category element software.
softwareItem
Abstract Datatype property for software items.
reference_to_software
cross-reference to software
software.citation_id
This data item is a pointer to attribute id in category citation in the CITATION
category.
software.classification
The classification of the program according to its
major function.
data collection
data reduction
phasing
model building
refinement
validation
other
software.compiler_name
The compiler used to compile the software.
Convex Fortran
gcc
DEC C
software.compiler_version
The version of the compiler used to compile the software.
3.1
2.1 alpha
software.contact_author
The recognized contact author of the software. This could be
the original author, someone who has modified the code or
someone who maintains the code. It should be the person
most commonly associated with the code.
T. Alwyn Jones
Axel Brunger
software.contact_author_email
The e-mail address of the person specified in
attribute contact_author in category software.
bourne@sdsc.edu
software.date
The date the software was released.
1991-10-01
1990-04-30
software.dependencies
Any prerequisite software required to run attribute name in category software.
PDBlib class library
software.description
Description of the software.
Uses method of restrained least squares
software.hardware
The hardware upon which the software was run.
Sun Sparc 10 model 41
Dec Alpha 3000 model 500S
Silicon Graphics Elan
Compaq PC 486/66
Ada
assembler
Awk
Basic
C++
C/C++
C
csh
Fortran
Fortran_77
Fortran 77
Fortran 90
Java
Java & Fortran
ksh
Pascal
Perl
Python
sh
Tcl
Other
The major computing language in which the software is
coded.
software.location
The URL for an Internet address at which
details of the software can be found.
http://rosebud.sdsc.edu/projects/pb/IUCr/software.html
ftp://ftp.sdsc.edu/pub/sdsc/biology/
software.mods
Any noteworthy modifications to the base software, if applicable.
Added support for space group F432
software.name
The name of the software.
Merlot
O
Xengen
X-plor
software.os
The name of the operating system under which the software
runs.
Ultrix
OpenVMS
DOS
Windows 95
Windows NT
Irix
HPUX
DEC Unix
software.os_version
The version of the operating system under which the software
runs.
3.1
4.2.1
program
library
package
filter
jiffy
other
The classification of the software according to the most
common types.
software.version
The version of the software.
v1.0
beta
3.1-2
unknown
software.pdbx_ordinal
An ordinal index for this category
1
2
space_group
Contains all the data items that refer to the space group as a
whole, such as its name or crystal system. They may be looped,
for example, in a list of space groups and their properties.
Only a subset of the SPACE_GROUP category items appear in
this dictionary. The remainder are found in the symmetry CIF
dictionary.
Space-group types are identified by their number as given in
International Tables for Crystallography Vol. A. Specific
settings of the space groups can be identified either by their
Hall symbol or by specifying their symmetry operations.
The commonly used Hermann-Mauguin symbol determines the
space-group type uniquely but several different Hermann-Mauguin
symbols may refer to the same space-group type. A Hermann-Mauguin
symbol contains information on the choice of the basis, but not
on the choice of origin. Different formats for the
Hermann-Mauguin symbol are found in the symmetry CIF dictionary.
Example 1 - the monoclinic space group No. 15 with unique axis b.
<PDBx:space_groupCategory>
<PDBx:space_group id="1">
<PDBx:IT_number>15</PDBx:IT_number>
<PDBx:crystal_system>monoclinic</PDBx:crystal_system>
<PDBx:name_H-M_alt>C 2/c</PDBx:name_H-M_alt>
<PDBx:name_Hall>-C 2yc</PDBx:name_Hall>
</PDBx:space_group>
</PDBx:space_groupCategory>
0
1
0
1
0
1
0
1
1
space_groupCategory
This property indicates that datablock
has a category element space_group.
space_groupItem
Abstract Datatype property for space_group items.
reference_to_space_group
cross-reference to space_group
space_group.IT_number
The number as assigned in International Tables for
Crystallography Vol. A, specifying the proper affine class (i.e.
the orientation-preserving affine class) of space groups
(crystallographic space-group type) to which the space group
belongs. This number defines the space-group type but not
the coordinate system in which it is expressed.
triclinic
monoclinic
orthorhombic
tetragonal
trigonal
hexagonal
cubic
The name of the system of geometric crystal classes of space
groups (crystal system) to which the space group belongs.
Note that rhombohedral space groups belong to the
trigonal system.
space_group.name_H-M_alt
attribute name_H-M_alt in category space_group allows any Hermann-Mauguin symbol
to be given. The way in which this item is used is determined
by the user and in general is not intended to be interpreted by
computer. It may, for example, be used to give one of the
extended Hermann-Mauguin symbols given in Table 4.3.2.1 of
International Tables for Crystallography Vol. A (2002) or
a Hermann-Mauguin symbol for a conventional or unconventional
setting.
Each component of the space-group name is separated by a
space or an underscore. The use of a space is strongly
recommended. The underscore is only retained because it
was used in old CIFs. It should not be
used in new CIFs. Subscripts should appear without special
symbols. Bars should be given as negative signs before the
numbers to which they apply.
The commonly used Hermann-Mauguin symbol determines the space-
group type uniquely but a given space-group type may be
described by more than one Hermann-Mauguin symbol. The space-
group type is best described using attribute IT_number.
in category space_group
The Hermann-Mauguin symbol may contain information on the
choice of basis, but not on the choice of origin. To
define the setting uniquely, use attribute name_Hall in category space_group or
list the symmetry operations.
three examples for space group No. 63
loop_
_space_group.name_H-M_alt
'C m c m'
'C 2/c 2/m 21/m'
'A m a m'
space_group.name_Hall
Space-group symbol defined by Hall.
Each component of the space-group name is separated by a
space or an underscore. The use of a space is strongly
recommended. The underscore is only retained because it
was used in old CIFs. It should not be
used in new CIFs.
attribute name_Hall in category space_group uniquely defines the space group and
its reference to a particular coordinate system.
Ref: Hall, S. R. (1981). Acta Cryst. A37, 517-525; erratum
(1981), A37, 921.
[See also International Tables for Crystallography
Vol. B (2001), Chapter 1.4, Appendix 1.4.2.]
equivalent to Pca21
P 2c -2ac
equivalent to Ia3d
-I 4bd 2ab 3
space_group.id
This is the unique identifier for the SPACE_GROUP category.
space_group_symop
Contains information about the symmetry operations of the
space group.
Example 1 - The symmetry operations for the space group P21/c.
<PDBx:space_group_symopCategory>
<PDBx:space_group_symop id="1">
<PDBx:operation_xyz>x,y,z</PDBx:operation_xyz>
</PDBx:space_group_symop>
<PDBx:space_group_symop id="2">
<PDBx:operation_xyz>-x,-y,-z</PDBx:operation_xyz>
</PDBx:space_group_symop>
<PDBx:space_group_symop id="3">
<PDBx:operation_xyz>-x,1/2+y,1/2-z</PDBx:operation_xyz>
</PDBx:space_group_symop>
<PDBx:space_group_symop id="4">
<PDBx:operation_xyz>x,1/2-y,1/2+z</PDBx:operation_xyz>
</PDBx:space_group_symop>
</PDBx:space_group_symopCategory>
0
1
0
1
1
space_group_symopCategory
This property indicates that datablock
has a category element space_group_symop.
space_group_symopItem
Abstract Datatype property for space_group_symop items.
reference_to_space_group_symop
cross-reference to space_group_symop
space_group_symop.operation_xyz
A parsable string giving one of the symmetry operations of the
space group in algebraic form. If W is a matrix representation
of the rotational part of the symmetry operation defined by the
positions and signs of x, y and z, and w is a column of
translations defined by the fractions, an equivalent position
X' is generated from a given position X by the equation
X' = WX + w
(Note: X is used to represent bold_italics_x in International
Tables for Crystallography Vol. A, Part 5)
When a list of symmetry operations is given, it must contain
a complete set of coordinate representatives which generates
all the operations of the space group by the addition of
all primitive translations of the space group. Such
representatives are to be found as the coordinates of
the general-equivalent position in International Tables for
Crystallography Vol. A (2002), to which it is necessary to
add any centring translations shown above the
general-equivalent position.
That is to say, it is necessary to list explicity all the
symmetry operations required to generate all the atoms in
the unit cell defined by the setting used.
glide reflection through the plane (x,1/4,z),
with glide vector 1/2 c
x,1/2-y,1/2+z
space_group_symop.sg_id
This must match a particular value of attribute id in category space_group, allowing
the symmetry operation to be identified with a particular space
group.
space_group_symop.id
An arbitrary identifier that uniquely labels each symmetry
operation in the list.
struct
Data items in the STRUCT category record details about the
description of the crystallographic structure.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:structCategory>
<PDBx:struct entry_id="5HVP">
<PDBx:title> HIV-1 protease complex with acetyl-pepstatin</PDBx:title>
</PDBx:struct>
</PDBx:structCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
structCategory
This property indicates that datablock
has a category element struct.
structItem
Abstract Datatype property for struct items.
reference_to_struct
cross-reference to struct
Y
N
The item indicates whether the entry is a CASP target, a CASD-NMR target,
or similar target participating in methods development experiments.
Y
struct.pdbx_descriptor
An automatically generated descriptor for an NDB structure or
the unstructured content of the PDB COMPND record.
5'-D(*CP*GP*CP*(HYD)AP*AP*AP*TP*TP*TP*GP*CP*G)-3'
struct.pdbx_formula_weight
Estimated formula mass in daltons of the
deposited structure assembly.
struct.pdbx_formula_weight_method
Method used to determine attribute pdbx_formula_weight in category struct.
MASS SPEC
CALCULATION
struct.pdbx_model_details
Text description of the methodology which produced this
model structure.
This model was produced from a 10 nanosecond Amber/MD simulation
starting from PDB structure ID 1ABC.
struct.pdbx_model_type_details
A description of the type of structure model.
MINIMIZED AVERAGE
struct.title
A title for the data block. The author should attempt to convey
the essence of the structure archived in the CIF in the title,
and to distinguish this structural result from others.
5'-D(*(I)CP*CP*GP*G)-3
T4 lysozyme mutant - S32A
hen egg white lysozyme at -30 degrees C
quail egg white lysozyme at 2 atmospheres
struct.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
struct_asym
Data items in the STRUCT_ASYM category record details about the
structural elements in the asymmetric unit.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:struct_asymCategory>
<PDBx:struct_asym id="A">
<PDBx:details>one monomer of the dimeric enzyme</PDBx:details>
<PDBx:entity_id>1</PDBx:entity_id>
</PDBx:struct_asym>
<PDBx:struct_asym id="B">
<PDBx:details>one monomer of the dimeric enzyme</PDBx:details>
<PDBx:entity_id>1</PDBx:entity_id>
</PDBx:struct_asym>
<PDBx:struct_asym id="C">
<PDBx:details>one partially occupied position for the inhibitor</PDBx:details>
<PDBx:entity_id>2</PDBx:entity_id>
</PDBx:struct_asym>
<PDBx:struct_asym id="D">
<PDBx:details>one partially occupied position for the inhibitor</PDBx:details>
<PDBx:entity_id>2</PDBx:entity_id>
</PDBx:struct_asym>
</PDBx:struct_asymCategory>
0
1
1
1
0
1
0
1
1
struct_asymCategory
This property indicates that datablock
has a category element struct_asym.
struct_asymItem
Abstract Datatype property for struct_asym items.
reference_to_struct_asym
cross-reference to struct_asym
struct_asym.details
A description of special aspects of this portion of the contents
of the asymmetric unit.
The drug binds to this enzyme in two roughly
twofold symmetric modes. Hence this
biological unit (3) is roughly twofold
symmetric to biological unit (2). Disorder in
the protein chain indicated with alternative
ID 2 should be used with this biological unit.
struct_asym.entity_id
This data item is a pointer to attribute id in category entity in the ENTITY category.
Y
N
A flag indicating that this entity was originally labeled
with a blank PDB chain id.
struct_asym.pdbx_modified
This data item indicates whether the structural elements are modified.
y
struct_asym.id
The value of attribute id in category struct_asym must uniquely identify a record in
the STRUCT_ASYM list.
Note that this item need not be a number; it can be any unique
identifier.
1
A
2B3
struct_biol
Data items in the STRUCT_BIOL category record details about
the structural elements that form each structure of biological
significance.
A given crystal structure may contain many different biological
structures. A given structural component in the asymmetric
unit may be part of more than one biological unit. A given
biological structure may involve crystallographic symmetry.
For instance, in a structure of a lysozyme-FAB structure, the
light- and heavy-chain components of the FAB could be one
biological unit, while the two chains of the FAB and the lysozyme
could constitute a second biological unit.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:struct_biolCategory>
<PDBx:struct_biol id="1">
<PDBx:details> significant deviations from twofold symmetry exist in this
dimeric enzyme</PDBx:details>
</PDBx:struct_biol>
<PDBx:struct_biol id="2">
<PDBx:details> The drug binds to this enzyme in two roughly twofold
symmetric modes. Hence this biological unit (2) is roughly
twofold symmetric to biological unit (3). Disorder in the
protein chain indicated with alternative ID 1 should be
used with this biological unit.</PDBx:details>
</PDBx:struct_biol>
<PDBx:struct_biol id="3">
<PDBx:details> The drug binds to this enzyme in two roughly twofold
symmetric modes. Hence this biological unit (3) is roughly
twofold symmetric to biological unit (2). Disorder in the
protein chain indicated with alternative ID 2 should be
used with this biological unit.</PDBx:details>
</PDBx:struct_biol>
</PDBx:struct_biolCategory>
0
1
0
1
0
1
0
1
0
1
0
1
1
struct_biolCategory
This property indicates that datablock
has a category element struct_biol.
struct_biolItem
Abstract Datatype property for struct_biol items.
reference_to_struct_biol
cross-reference to struct_biol
struct_biol.details
A description of special aspects of the biological unit.
The drug binds to this enzyme in two roughly
twofold symmetric modes. Hence this
biological unit (3) is roughly twofold
symmetric to biological unit (2). Disorder in
the protein chain indicated with alternative
ID 2 should be used with this biological unit.
MONOMER
DIMER
TRIMER
TETRAMER
HEXAMER
MORE
A description of the structural aggregation in this assembly.
struct_biol.pdbx_assembly_method
The method or experiment used to determine this assembly.
AUTHOR PROVIDED', 'LCMS', 'PISA', 'PQS
struct_biol.pdbx_formula_weight
Estimated formula mass in daltons of the
biological assembly.
struct_biol.pdbx_formula_weight_method
Method used to determine attribute pdbx_formula_weight in category struct_biol.
MASS SPEC
CALCULATION
struct_biol.pdbx_parent_biol_id
An identifier for the parent biological assembly
if this biological unit is part of a complex assembly.
1
2
3
struct_biol.id
The value of attribute id in category struct_biol must uniquely identify a record in
the STRUCT_BIOL list.
Note that this item need not be a number; it can be any unique
identifier.
struct_biol_gen
Data items in the STRUCT_BIOL_GEN category record details about
the generation of each biological unit. The STRUCT_BIOL_GEN
data items provide the specifications of the components that
constitute that biological unit, which may include symmetry
elements.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:struct_biol_genCategory>
<PDBx:struct_biol_gen asym_id="A" biol_id="1" symmetry="1_555"></PDBx:struct_biol_gen>
<PDBx:struct_biol_gen asym_id="B" biol_id="1" symmetry="1_555"></PDBx:struct_biol_gen>
<PDBx:struct_biol_gen asym_id="A" biol_id="2" symmetry="1_555"></PDBx:struct_biol_gen>
<PDBx:struct_biol_gen asym_id="B" biol_id="2" symmetry="1_555"></PDBx:struct_biol_gen>
<PDBx:struct_biol_gen asym_id="C" biol_id="2" symmetry="1_555"></PDBx:struct_biol_gen>
<PDBx:struct_biol_gen asym_id="A" biol_id="3" symmetry="1_555"></PDBx:struct_biol_gen>
<PDBx:struct_biol_gen asym_id="B" biol_id="3" symmetry="1_555"></PDBx:struct_biol_gen>
<PDBx:struct_biol_gen asym_id="D" biol_id="3" symmetry="1_555"></PDBx:struct_biol_gen>
</PDBx:struct_biol_genCategory>
0
1
0
1
0
1
1
1
1
struct_biol_genCategory
This property indicates that datablock
has a category element struct_biol_gen.
struct_biol_genItem
Abstract Datatype property for struct_biol_gen items.
reference_to_struct_biol_gen
cross-reference to struct_biol_gen
struct_biol_gen.details
A description of special aspects of the symmetry generation of
this portion of the biological structure.
The zinc atom lies on a special position;
application of symmetry elements to generate
the insulin hexamer will generate excess zinc
atoms, which must be removed by hand.
struct_biol_gen.pdbx_PDB_order
An ordering index used to reproduce the presentation of
chain order in the original PDB format data files.
1
2
3
struct_biol_gen.pdbx_full_symmetry_operation
This item expresses category attribute symmetry
in category struct_biol_gen on an X, Y and Z basis.
-X, Y+1/2, -Z
struct_biol_gen.asym_id
This data item is a pointer to attribute id in category struct_asym in the STRUCT_ASYM
category.
struct_biol_gen.biol_id
This data item is a pointer to attribute id in category struct_biol in the STRUCT_BIOL
category.
struct_biol_gen.symmetry
Describes the symmetry operation that should be applied to the
atom set specified by attribute asym_id in category struct_biol_gen to generate a
portion of the biological structure.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
struct_biol_keywords
Data items in the STRUCT_BIOL_KEYWORDS category record
keywords that describe each biological unit.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:struct_biol_keywordsCategory>
<PDBx:struct_biol_keywords biol_id="1" text="aspartyl-protease"></PDBx:struct_biol_keywords>
<PDBx:struct_biol_keywords biol_id="1" text="aspartic-protease"></PDBx:struct_biol_keywords>
<PDBx:struct_biol_keywords biol_id="1" text="acid-protease"></PDBx:struct_biol_keywords>
<PDBx:struct_biol_keywords biol_id="1" text="aspartyl-proteinase"></PDBx:struct_biol_keywords>
<PDBx:struct_biol_keywords biol_id="1" text="aspartic-proteinase"></PDBx:struct_biol_keywords>
<PDBx:struct_biol_keywords biol_id="1" text="acid-proteinase"></PDBx:struct_biol_keywords>
<PDBx:struct_biol_keywords biol_id="1" text="enzyme"></PDBx:struct_biol_keywords>
<PDBx:struct_biol_keywords biol_id="1" text="protease"></PDBx:struct_biol_keywords>
<PDBx:struct_biol_keywords biol_id="1" text="proteinase"></PDBx:struct_biol_keywords>
<PDBx:struct_biol_keywords biol_id="1" text="dimer"></PDBx:struct_biol_keywords>
<PDBx:struct_biol_keywords biol_id="2" text="drug-enzyme complex"></PDBx:struct_biol_keywords>
<PDBx:struct_biol_keywords biol_id="2" text="inhibitor-enzyme complex"></PDBx:struct_biol_keywords>
<PDBx:struct_biol_keywords biol_id="2" text="drug-protease complex"></PDBx:struct_biol_keywords>
<PDBx:struct_biol_keywords biol_id="2" text="inhibitor-protease complex"></PDBx:struct_biol_keywords>
<PDBx:struct_biol_keywords biol_id="3" text="drug-enzyme complex"></PDBx:struct_biol_keywords>
<PDBx:struct_biol_keywords biol_id="3" text="inhibitor-enzyme complex"></PDBx:struct_biol_keywords>
<PDBx:struct_biol_keywords biol_id="3" text="drug-protease complex"></PDBx:struct_biol_keywords>
<PDBx:struct_biol_keywords biol_id="3" text="inhibitor-protease complex"></PDBx:struct_biol_keywords>
</PDBx:struct_biol_keywordsCategory>
1
1
struct_biol_keywordsCategory
This property indicates that datablock
has a category element struct_biol_keywords.
struct_biol_keywordsItem
Abstract Datatype property for struct_biol_keywords items.
reference_to_struct_biol_keywords
cross-reference to struct_biol_keywords
struct_biol_keywords.biol_id
This data item is a pointer to attribute id in category struct_biol in the STRUCT_BIOL
category.
struct_biol_keywords.text
Keywords describing this biological entity.
antibody
antigen
enzyme
cytokine
tRNA
struct_biol_view
Data items in the STRUCT_BIOL_VIEW category record details
about how to draw and annotate an informative view of the
biological structure.
Example 1 - based on NDB structure GDL001 by Coll, Aymami,
Van Der Marel, Van Boom, Rich & Wang
[Biochemistry, (1989), 28, 310-320].
<PDBx:struct_biol_viewCategory>
<PDBx:struct_biol_view biol_id="c1" id="1">
<PDBx:details> This view highlights the ATAT-Netropsin interaction in the
DNA-drug complex.</PDBx:details>
<PDBx:rot_matrix11>0.132</PDBx:rot_matrix11>
<PDBx:rot_matrix12>0.922</PDBx:rot_matrix12>
<PDBx:rot_matrix13>-0.363</PDBx:rot_matrix13>
<PDBx:rot_matrix21>0.131</PDBx:rot_matrix21>
<PDBx:rot_matrix22>-0.380</PDBx:rot_matrix22>
<PDBx:rot_matrix23>-0.916</PDBx:rot_matrix23>
<PDBx:rot_matrix31>-0.982</PDBx:rot_matrix31>
<PDBx:rot_matrix32>0.073</PDBx:rot_matrix32>
<PDBx:rot_matrix33>-0.172</PDBx:rot_matrix33>
</PDBx:struct_biol_view>
</PDBx:struct_biol_viewCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
struct_biol_viewCategory
This property indicates that datablock
has a category element struct_biol_view.
struct_biol_viewItem
Abstract Datatype property for struct_biol_view items.
reference_to_struct_biol_view
cross-reference to struct_biol_view
struct_biol_view.details
A description of special aspects of this view of the biological
structure.
This data item can be used as a figure legend.
The enzyme has been oriented with the
molecular twofold axis aligned with the
horizontal axis of the figure.
struct_biol_view.rot_matrix11
The [1][1] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_BIOL_GEN category to give a view useful for describing the
structure. The conventions used in the rotation are described in
attribute details.
in category struct_biol_view
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
struct_biol_view.rot_matrix12
The [1][2] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_BIOL_GEN category to give a view useful for describing the
structure. The conventions used in the rotation are described in
attribute details.
in category struct_biol_view
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
struct_biol_view.rot_matrix13
The [1][3] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_BIOL_GEN category to give a view useful for describing the
structure. The conventions used in the rotation are described in
attribute details.
in category struct_biol_view
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
struct_biol_view.rot_matrix21
The [2][1] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_BIOL_GEN category to give a view useful for describing the
structure. The conventions used in the rotation are described in
attribute details.
in category struct_biol_view
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
struct_biol_view.rot_matrix22
The [2][2] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_BIOL_GEN category to give a view useful for describing the
structure. The conventions used in the rotation are described in
attribute details.
in category struct_biol_view
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
struct_biol_view.rot_matrix23
The [2][3] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_BIOL_GEN category to give a view useful for describing the
structure. The conventions used in the rotation are described in
attribute details.
in category struct_biol_view
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
struct_biol_view.rot_matrix31
The [3][1] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_BIOL_GEN category to give a view useful for describing the
structure. The conventions used in the rotation are described in
attribute details.
in category struct_biol_view
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
struct_biol_view.rot_matrix32
The [3][2] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_BIOL_GEN category to give a view useful for describing the
structure. The conventions used in the rotation are described in
attribute details.
in category struct_biol_view
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
struct_biol_view.rot_matrix33
The [3][3] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_BIOL_GEN category to give a view useful for describing the
structure. The conventions used in the rotation are described in
attribute details.
in category struct_biol_view
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
struct_biol_view.biol_id
This data item is a pointer to attribute id in category struct_biol in the STRUCT_BIOL
category.
struct_biol_view.id
The value of attribute id in category struct_biol_view must uniquely identify a
record in the STRUCT_BIOL_VIEW list.
Note that this item need not be a number; it can be any unique
identifier.
Figure 1
unliganded enzyme
view down enzyme active site
struct_conf
Data items in the STRUCT_CONF category record details about
the backbone conformation of a segment of polymer.
Data items in the STRUCT_CONF_TYPE category define the
criteria used to identify the backbone conformations.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:struct_confCategory>
<PDBx:struct_conf id="HELX1">
<PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id>
<PDBx:beg_label_comp_id>ARG</PDBx:beg_label_comp_id>
<PDBx:beg_label_seq_id>87</PDBx:beg_label_seq_id>
<PDBx:conf_type_id>HELX_RH_AL_P</PDBx:conf_type_id>
<PDBx:details></PDBx:details>
<PDBx:end_label_asym_id>A</PDBx:end_label_asym_id>
<PDBx:end_label_comp_id>GLN</PDBx:end_label_comp_id>
<PDBx:end_label_seq_id>92</PDBx:end_label_seq_id>
</PDBx:struct_conf>
<PDBx:struct_conf id="HELX2">
<PDBx:beg_label_asym_id>B</PDBx:beg_label_asym_id>
<PDBx:beg_label_comp_id>ARG</PDBx:beg_label_comp_id>
<PDBx:beg_label_seq_id>287</PDBx:beg_label_seq_id>
<PDBx:conf_type_id>HELX_RH_AL_P</PDBx:conf_type_id>
<PDBx:details></PDBx:details>
<PDBx:end_label_asym_id>B</PDBx:end_label_asym_id>
<PDBx:end_label_comp_id>GLN</PDBx:end_label_comp_id>
<PDBx:end_label_seq_id>292</PDBx:end_label_seq_id>
</PDBx:struct_conf>
<PDBx:struct_conf id="STRN1">
<PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id>
<PDBx:beg_label_comp_id>PRO</PDBx:beg_label_comp_id>
<PDBx:beg_label_seq_id>1</PDBx:beg_label_seq_id>
<PDBx:conf_type_id>STRN_P</PDBx:conf_type_id>
<PDBx:details></PDBx:details>
<PDBx:end_label_asym_id>A</PDBx:end_label_asym_id>
<PDBx:end_label_comp_id>LEU</PDBx:end_label_comp_id>
<PDBx:end_label_seq_id>5</PDBx:end_label_seq_id>
</PDBx:struct_conf>
<PDBx:struct_conf id="STRN2">
<PDBx:beg_label_asym_id>B</PDBx:beg_label_asym_id>
<PDBx:beg_label_comp_id>CYS</PDBx:beg_label_comp_id>
<PDBx:beg_label_seq_id>295</PDBx:beg_label_seq_id>
<PDBx:conf_type_id>STRN_P</PDBx:conf_type_id>
<PDBx:details></PDBx:details>
<PDBx:end_label_asym_id>B</PDBx:end_label_asym_id>
<PDBx:end_label_comp_id>PHE</PDBx:end_label_comp_id>
<PDBx:end_label_seq_id>299</PDBx:end_label_seq_id>
</PDBx:struct_conf>
<PDBx:struct_conf id="STRN3">
<PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id>
<PDBx:beg_label_comp_id>CYS</PDBx:beg_label_comp_id>
<PDBx:beg_label_seq_id>95</PDBx:beg_label_seq_id>
<PDBx:conf_type_id>STRN_P</PDBx:conf_type_id>
<PDBx:details></PDBx:details>
<PDBx:end_label_asym_id>A</PDBx:end_label_asym_id>
<PDBx:end_label_comp_id>PHE</PDBx:end_label_comp_id>
<PDBx:end_label_seq_id>299</PDBx:end_label_seq_id>
</PDBx:struct_conf>
<PDBx:struct_conf id="STRN4">
<PDBx:beg_label_asym_id>B</PDBx:beg_label_asym_id>
<PDBx:beg_label_comp_id>PRO</PDBx:beg_label_comp_id>
<PDBx:beg_label_seq_id>201</PDBx:beg_label_seq_id>
<PDBx:conf_type_id>STRN_P</PDBx:conf_type_id>
<PDBx:details></PDBx:details>
<PDBx:end_label_asym_id>B</PDBx:end_label_asym_id>
<PDBx:end_label_comp_id>LEU</PDBx:end_label_comp_id>
<PDBx:end_label_seq_id>205</PDBx:end_label_seq_id>
</PDBx:struct_conf>
<PDBx:struct_conf id="TURN1">
<PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id>
<PDBx:beg_label_comp_id>ILE</PDBx:beg_label_comp_id>
<PDBx:beg_label_seq_id>15</PDBx:beg_label_seq_id>
<PDBx:conf_type_id>TURN_TY1P_P</PDBx:conf_type_id>
<PDBx:details></PDBx:details>
<PDBx:end_label_asym_id>A</PDBx:end_label_asym_id>
<PDBx:end_label_comp_id>GLN</PDBx:end_label_comp_id>
<PDBx:end_label_seq_id>18</PDBx:end_label_seq_id>
</PDBx:struct_conf>
<PDBx:struct_conf id="TURN2">
<PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id>
<PDBx:beg_label_comp_id>GLY</PDBx:beg_label_comp_id>
<PDBx:beg_label_seq_id>49</PDBx:beg_label_seq_id>
<PDBx:conf_type_id>TURN_TY2_P</PDBx:conf_type_id>
<PDBx:details></PDBx:details>
<PDBx:end_label_asym_id>A</PDBx:end_label_asym_id>
<PDBx:end_label_comp_id>GLY</PDBx:end_label_comp_id>
<PDBx:end_label_seq_id>52</PDBx:end_label_seq_id>
</PDBx:struct_conf>
<PDBx:struct_conf id="TURN3">
<PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id>
<PDBx:beg_label_comp_id>ILE</PDBx:beg_label_comp_id>
<PDBx:beg_label_seq_id>55</PDBx:beg_label_seq_id>
<PDBx:conf_type_id>TURN_TY1P_P</PDBx:conf_type_id>
<PDBx:details></PDBx:details>
<PDBx:end_label_asym_id>A</PDBx:end_label_asym_id>
<PDBx:end_label_comp_id>HIS</PDBx:end_label_comp_id>
<PDBx:end_label_seq_id>69</PDBx:end_label_seq_id>
</PDBx:struct_conf>
<PDBx:struct_conf id="TURN4">
<PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id>
<PDBx:beg_label_comp_id>THR</PDBx:beg_label_comp_id>
<PDBx:beg_label_seq_id>91</PDBx:beg_label_seq_id>
<PDBx:conf_type_id>TURN_TY1_P</PDBx:conf_type_id>
<PDBx:details></PDBx:details>
<PDBx:end_label_asym_id>A</PDBx:end_label_asym_id>
<PDBx:end_label_comp_id>GLY</PDBx:end_label_comp_id>
<PDBx:end_label_seq_id>94</PDBx:end_label_seq_id>
</PDBx:struct_conf>
</PDBx:struct_confCategory>
0
1
0
1
0
1
1
1
1
1
1
1
1
1
0
1
0
1
0
1
0
1
1
1
1
1
1
1
0
1
0
1
0
1
0
1
0
1
1
struct_confCategory
This property indicates that datablock
has a category element struct_conf.
struct_confItem
Abstract Datatype property for struct_conf items.
reference_to_struct_conf
cross-reference to struct_conf
struct_conf.beg_auth_asym_id
A component of the identifier for the residue at which the
conformation segment begins.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
struct_conf.beg_auth_comp_id
A component of the identifier for the residue at which the
conformation segment begins.
This data item is a pointer to attribute auth_comp_id in category atom_site in
the ATOM_SITE category.
struct_conf.beg_auth_seq_id
A component of the identifier for the residue at which the
conformation segment begins.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
struct_conf.beg_label_asym_id
A component of the identifier for the residue at which the
conformation segment begins.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
struct_conf.beg_label_comp_id
A component of the identifier for the residue at which the
conformation segment begins.
This data item is a pointer to attribute label_comp_id in category atom_site in
the ATOM_SITE category.
struct_conf.beg_label_seq_id
A component of the identifier for the residue at which the
conformation segment begins.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
struct_conf.conf_type_id
This data item is a pointer to attribute id in category struct_conf_type in the
STRUCT_CONF_TYPE category.
struct_conf.details
A description of special aspects of the conformation assignment.
struct_conf.end_auth_asym_id
A component of the identifier for the residue at which the
conformation segment ends.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
struct_conf.end_auth_comp_id
A component of the identifier for the residue at which the
conformation segment ends.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
struct_conf.end_auth_seq_id
A component of the identifier for the residue at which the
conformation segment ends.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
struct_conf.end_label_asym_id
A component of the identifier for the residue at which the
conformation segment ends.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
struct_conf.end_label_comp_id
A component of the identifier for the residue at which the
conformation segment ends.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
struct_conf.end_label_seq_id
A component of the identifier for the residue at which the
conformation segment ends.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
struct_conf.pdbx_PDB_helix_class
This item is a place holder for the helix class used in the PDB
HELIX record.
struct_conf.pdbx_PDB_helix_id
A placeholder for the helix identifier of the PDB
HELIX record.
struct_conf.pdbx_PDB_helix_length
A placeholder for the lengths of the helix of the PDB
HELIX record.
struct_conf.pdbx_beg_PDB_ins_code
A component of the identifier for the residue at which the
conformation segment starts.
struct_conf.pdbx_end_PDB_ins_code
A component of the identifier for the residue at which the
conformation segment ends.
struct_conf.id
The value of attribute id in category struct_conf must uniquely identify a record in
the STRUCT_CONF list.
Note that this item need not be a number; it can be any unique
identifier.
struct_conf_type
Data items in the STRUCT_CONF_TYPE category record details
about the criteria used to identify backbone conformations of a
segment of polymer.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:struct_conf_typeCategory>
<PDBx:struct_conf_type id="HELX_RH_AL_P">
<PDBx:criteria>author judgement</PDBx:criteria>
<PDBx:reference></PDBx:reference>
</PDBx:struct_conf_type>
<PDBx:struct_conf_type id="STRN_P">
<PDBx:criteria>author judgement</PDBx:criteria>
<PDBx:reference></PDBx:reference>
</PDBx:struct_conf_type>
<PDBx:struct_conf_type id="TURN_TY1_P">
<PDBx:criteria>author judgement</PDBx:criteria>
<PDBx:reference></PDBx:reference>
</PDBx:struct_conf_type>
<PDBx:struct_conf_type id="TURN_TY1P_P">
<PDBx:criteria>author judgement</PDBx:criteria>
<PDBx:reference></PDBx:reference>
</PDBx:struct_conf_type>
<PDBx:struct_conf_type id="TURN_TY2_P">
<PDBx:criteria>author judgement</PDBx:criteria>
<PDBx:reference></PDBx:reference>
</PDBx:struct_conf_type>
<PDBx:struct_conf_type id="TURN_TY2P_P">
<PDBx:criteria>author judgement</PDBx:criteria>
<PDBx:reference></PDBx:reference>
</PDBx:struct_conf_type>
</PDBx:struct_conf_typeCategory>
0
1
0
1
1
struct_conf_typeCategory
This property indicates that datablock
has a category element struct_conf_type.
struct_conf_typeItem
Abstract Datatype property for struct_conf_type items.
reference_to_struct_conf_type
cross-reference to struct_conf_type
struct_conf_type.criteria
The criteria used to assign this conformation type.
author judgement
phi=54-74, psi=30-50
struct_conf_type.reference
A literature reference that defines the criteria used to assign
this conformation type and subtype.
HELX_P
HELX_OT_P
HELX_RH_P
HELX_RH_OT_P
HELX_RH_AL_P
HELX_RH_GA_P
HELX_RH_OM_P
HELX_RH_PI_P
HELX_RH_27_P
HELX_RH_3T_P
HELX_RH_PP_P
HELX_LH_P
HELX_LH_OT_P
HELX_LH_AL_P
HELX_LH_GA_P
HELX_LH_OM_P
HELX_LH_PI_P
HELX_LH_27_P
HELX_LH_3T_P
HELX_LH_PP_P
HELX_N
HELX_OT_N
HELX_RH_N
HELX_RH_OT_N
HELX_RH_A_N
HELX_RH_B_N
HELX_RH_Z_N
HELX_LH_N
HELX_LH_OT_N
HELX_LH_A_N
HELX_LH_B_N
HELX_LH_Z_N
TURN_P
TURN_OT_P
TURN_TY1_P
TURN_TY1P_P
TURN_TY2_P
TURN_TY2P_P
TURN_TY3_P
TURN_TY3P_P
STRN
The descriptor that categorizes the type of the conformation
of the backbone of the polymer (whether protein or nucleic acid).
Explicit values for the torsion angles that define each
conformation are not given here, but it is expected that the
author would provide such information in either the
_struct_conf_type.criteria or _struct_conf_type.reference data
items, or both.
struct_conn
Data items in the STRUCT_CONN category record details about
the connections between portions of the structure. These can be
hydrogen bonds, salt bridges, disulfide bridges and so on.
The STRUCT_CONN_TYPE records define the criteria used to
identify these connections.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:struct_connCategory>
<PDBx:struct_conn id="C1">
<PDBx:conn_type_id>saltbr</PDBx:conn_type_id>
<PDBx:details></PDBx:details>
<PDBx:ptnr1_label_asym_id>A</PDBx:ptnr1_label_asym_id>
<PDBx:ptnr1_label_atom_id>NZ1</PDBx:ptnr1_label_atom_id>
<PDBx:ptnr1_label_comp_id>ARG</PDBx:ptnr1_label_comp_id>
<PDBx:ptnr1_label_seq_id>87</PDBx:ptnr1_label_seq_id>
<PDBx:ptnr1_role>positive</PDBx:ptnr1_role>
<PDBx:ptnr1_symmetry>1_555</PDBx:ptnr1_symmetry>
<PDBx:ptnr2_label_asym_id>A</PDBx:ptnr2_label_asym_id>
<PDBx:ptnr2_label_atom_id>OE1</PDBx:ptnr2_label_atom_id>
<PDBx:ptnr2_label_comp_id>GLU</PDBx:ptnr2_label_comp_id>
<PDBx:ptnr2_label_seq_id>92</PDBx:ptnr2_label_seq_id>
<PDBx:ptnr2_role>negative</PDBx:ptnr2_role>
<PDBx:ptnr2_symmetry>1_555</PDBx:ptnr2_symmetry>
</PDBx:struct_conn>
<PDBx:struct_conn id="C2">
<PDBx:conn_type_id>hydrog</PDBx:conn_type_id>
<PDBx:details></PDBx:details>
<PDBx:ptnr1_label_asym_id>B</PDBx:ptnr1_label_asym_id>
<PDBx:ptnr1_label_atom_id>N</PDBx:ptnr1_label_atom_id>
<PDBx:ptnr1_label_comp_id>ARG</PDBx:ptnr1_label_comp_id>
<PDBx:ptnr1_label_seq_id>287</PDBx:ptnr1_label_seq_id>
<PDBx:ptnr1_role>donor</PDBx:ptnr1_role>
<PDBx:ptnr1_symmetry>1_555</PDBx:ptnr1_symmetry>
<PDBx:ptnr2_label_asym_id>B</PDBx:ptnr2_label_asym_id>
<PDBx:ptnr2_label_atom_id>O</PDBx:ptnr2_label_atom_id>
<PDBx:ptnr2_label_comp_id>GLY</PDBx:ptnr2_label_comp_id>
<PDBx:ptnr2_label_seq_id>292</PDBx:ptnr2_label_seq_id>
<PDBx:ptnr2_role>acceptor</PDBx:ptnr2_role>
<PDBx:ptnr2_symmetry>1_555</PDBx:ptnr2_symmetry>
</PDBx:struct_conn>
</PDBx:struct_connCategory>
1
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
0
1
1
1
1
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
0
1
1
1
1
1
0
1
0
1
1
struct_connCategory
This property indicates that datablock
has a category element struct_conn.
struct_connItem
Abstract Datatype property for struct_conn items.
reference_to_struct_conn
cross-reference to struct_conn
struct_conn.conn_type_id
This data item is a pointer to attribute id in category struct_conn_type in the
STRUCT_CONN_TYPE category.
struct_conn.details
A description of special aspects of the connection.
disulfide bridge C-S-S-C is highly distorted
struct_conn.pdbx_PDB_id
A placeholder for the PDB id in the case the category
is used to hold the information of the MODRES record of
a PDB file.
1ABC
struct_conn.pdbx_dist_value
Distance value for this contact.
struct_conn.pdbx_ptnr1_PDB_ins_code
A component of the identifier for partner 1 of the structure
connection.
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the
ATOM_SITE category.
1
2
struct_conn.pdbx_ptnr1_auth_alt_id
A component of the identifier for partner 1 of the
structure connection. This data item is a pointer to
attribute pdbx_auth_alt_id in category atom_site in the ATOM_SITE category.
A
B
struct_conn.pdbx_ptnr1_label_alt_id
A component of the identifier for partner 1 of the
structure connection. This data item is a pointer to
attribute label_alt_id in category atom_site in the ATOM_SITE category.
A
B
struct_conn.pdbx_ptnr1_standard_comp_id
A placeholder for the standard residue name found in
the MODRES record of a PDB file.
A
T
C
G
GLY
ALA
MET
struct_conn.pdbx_ptnr2_PDB_ins_code
A component of the identifier for partner 1 of the structure
connection.
This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the
ATOM_SITE category.
1
2
struct_conn.pdbx_ptnr2_auth_alt_id
A component of the identifier for partner 2 of the
structure connection. This data item is a pointer to
attribute pdbx_auth_alt_id in category atom_site in the ATOM_SITE category.
A
B
struct_conn.pdbx_ptnr2_label_alt_id
A component of the identifier for partner 2 of the
structure connection. This data item is a pointer to
attribute label_alt_id in category atom_site in the ATOM_SITE category.
A
B
struct_conn.pdbx_ptnr3_PDB_ins_code
A component of the identifier for partner 3 of the
structure connection. This data item is a pointer to
attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category.
1
2
struct_conn.pdbx_ptnr3_auth_alt_id
A component of the identifier for partner 3 of the
structure connection. This data item is a pointer to
attribute pdbx_auth_alt_id in category atom_site in the ATOM_SITE category.
A
B
struct_conn.pdbx_ptnr3_auth_asym_id
A component of the identifier for partner 3 of the
structure connection. This data item is a pointer to
attribute auth_asym_id in category atom_site in the ATOM_SITE category.
A
B
C
struct_conn.pdbx_ptnr3_auth_atom_id
A component of the identifier for partner 3 of the
structure connection. This data item is a pointer to
attribute auth_atom_id in category atom_site in the ATOM_SITE category.
O5*
struct_conn.pdbx_ptnr3_auth_comp_id
A component of the identifier for partner 3 of the
structure connection. This data item is a pointer to
attribute auth_comp_id in category atom_site in the ATOM_SITE category.
A
T
C
G
GLY
ALA
MET
struct_conn.pdbx_ptnr3_auth_seq_id
A component of the identifier for partner 1 of the
structure connection. This data item is a pointer to
attribute auth_seq_id in category atom_site in the ATOM_SITE category.
12
struct_conn.pdbx_ptnr3_label_alt_id
A component of the identifier for partner 3 of the
structure connection. This data item is a pointer to
attribute label_alt_id in category atom_site in the ATOM_SITE category.
A
B
struct_conn.pdbx_ptnr3_label_asym_id
A component of the identifier for partner 3 of the
structure connection. This data item is a pointer to
attribute label_asym_id in category atom_site in the ATOM_SITE category.
A
B
C
struct_conn.pdbx_ptnr3_label_atom_id
A component of the identifier for partner 3 of the
structure connection. This data item is a pointer to
attribute label_atom_id in category atom_site in the ATOM_SITE category.
O5*
struct_conn.pdbx_ptnr3_label_comp_id
A component of the identifier for partner 3 of the
structure connection. This data item is a pointer to
attribute label_comp_id in category atom_site in the ATOM_SITE category.
A
T
C
G
GLY
ALA
MET
struct_conn.pdbx_ptnr3_label_seq_id
A component of the identifier for partner 1 of the
structure connection. This data item is a pointer to
attribute label_seq_id in category atom_site in the ATOM_SITE category.
12
sing
doub
trip
quad
The chemical bond order associated with the specified atoms in
this contact.
struct_conn.ptnr1_auth_asym_id
A component of the identifier for partner 1 of the structure
connection.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
struct_conn.ptnr1_auth_atom_id
A component of the identifier for partner 1 of the structure
connection.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
struct_conn.ptnr1_auth_comp_id
A component of the identifier for partner 1 of the structure
connection.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
struct_conn.ptnr1_auth_seq_id
A component of the identifier for partner 1 of the structure
connection.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
struct_conn.ptnr1_label_alt_id
A component of the identifier for partner 1 of the structure
connection.
This data item is a pointer to attribute id in category atom_sites_alt in the
ATOM_SITES_ALT category.
struct_conn.ptnr1_label_asym_id
A component of the identifier for partner 1 of the structure
connection.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
struct_conn.ptnr1_label_atom_id
A component of the identifier for partner 1 of the structure
connection.
This data item is a pointer to attribute atom_id in category chem_comp_atom in the
CHEM_COMP_ATOM category.
struct_conn.ptnr1_label_comp_id
A component of the identifier for partner 1 of the structure
connection.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
struct_conn.ptnr1_label_seq_id
A component of the identifier for partner 1 of the structure
connection.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
struct_conn.ptnr1_role
The chemical or structural role of the first partner in
the structure connection.
donor
acceptor
negative
positive
metal
metal coordination
struct_conn.ptnr1_symmetry
Describes the symmetry operation that should be applied to the
atom set specified by attribute ptnr1_label* in category struct_conn to generate the
first partner in the structure connection.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
struct_conn.ptnr2_auth_asym_id
A component of the identifier for partner 2 of the structure
connection.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
struct_conn.ptnr2_auth_atom_id
A component of the identifier for partner 2 of the structure
connection.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
struct_conn.ptnr2_auth_comp_id
A component of the identifier for partner 2 of the structure
connection.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
struct_conn.ptnr2_auth_seq_id
A component of the identifier for partner 2 of the structure
connection.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
struct_conn.ptnr2_label_alt_id
A component of the identifier for partner 2 of the structure
connection.
This data item is a pointer to attribute id in category atom_sites_alt in the
ATOM_SITES_ALT category.
struct_conn.ptnr2_label_asym_id
A component of the identifier for partner 2 of the structure
connection.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
struct_conn.ptnr2_label_atom_id
A component of the identifier for partner 2 of the structure
connection.
This data item is a pointer to attribute atom_id in category chem_comp_atom in the
CHEM_COMP_ATOM category.
struct_conn.ptnr2_label_comp_id
A component of the identifier for partner 2 of the structure
connection.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
struct_conn.ptnr2_label_seq_id
A component of the identifier for partner 2 of the structure
connection.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
struct_conn.ptnr2_role
The chemical or structural role of the second partner in
the structure connection.
donor
acceptor
negative
positive
metal
metal coordination
struct_conn.ptnr2_symmetry
Describes the symmetry operation that should be applied to the
atom set specified by attribute ptnr2_label* in category struct_conn to generate the
second partner in the structure connection.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
struct_conn.id
The value of attribute id in category struct_conn must uniquely identify a record in
the STRUCT_CONN list.
Note that this item need not be a number; it can be any unique
identifier.
struct_conn_type
Data items in the STRUCT_CONN_TYPE category record details
about the criteria used to identify interactions between
portions of the structure.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:struct_conn_typeCategory>
<PDBx:struct_conn_type id="saltbr">
<PDBx:criteria>negative to positive distance > 2.5 \%A, < 3.2 \%A</PDBx:criteria>
<PDBx:reference></PDBx:reference>
</PDBx:struct_conn_type>
<PDBx:struct_conn_type id="hydrog">
<PDBx:criteria>NO distance > 2.5\%A, < 3.5\%A, NOC angle < 120 degrees</PDBx:criteria>
<PDBx:reference></PDBx:reference>
</PDBx:struct_conn_type>
</PDBx:struct_conn_typeCategory>
0
1
0
1
1
struct_conn_typeCategory
This property indicates that datablock
has a category element struct_conn_type.
struct_conn_typeItem
Abstract Datatype property for struct_conn_type items.
reference_to_struct_conn_type
cross-reference to struct_conn_type
struct_conn_type.criteria
The criteria used to define the interaction.
O to N distance > 2.5 \%A, < 3.2 \%A
authors judgement
struct_conn_type.reference
A reference that specifies the criteria used to define the
interaction.
covale
disulf
hydrog
metalc
mismat
saltbr
modres
covale_base
covale_sugar
covale_phosphate
The chemical or structural type of the interaction.
struct_keywords
Data items in the STRUCT_KEYWORDS category specify keywords
that describe the chemical structure in this entry.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:struct_keywordsCategory>
<PDBx:struct_keywords entry_id="5HVP">
<PDBx:text>enzyme-inhibitor complex, aspartyl protease, static disorder</PDBx:text>
</PDBx:struct_keywords>
</PDBx:struct_keywordsCategory>
0
1
0
1
1
struct_keywordsCategory
This property indicates that datablock
has a category element struct_keywords.
struct_keywordsItem
Abstract Datatype property for struct_keywords items.
reference_to_struct_keywords
cross-reference to struct_keywords
struct_keywords.pdbx_keywords
DNA
RNA
T-RNA
DNA/RNA
RIBOZYME
PROTEIN/DNA
PROTEIN/RNA
PEPTIDE NUCLEIC ACID
PEPTIDE NUCLEIC ACID/DNA
DNA-BINDING PROTEIN
RNA-BINDING PROTEIN
struct_keywords.text
Keywords describing this structure.
serine protease
inhibited complex
high-resolution refinement
struct_keywords.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
struct_mon_details
Data items in the STRUCT_MON_DETAILS category record details
about specifics of calculations summarized in data items in the
STRUCT_MON_PROT and STRUCT_MON_NUCL categories. These can
include the coefficients used in map calculations,
the radii used for including points in a calculation and so on.
0
1
0
1
0
1
1
struct_mon_detailsCategory
This property indicates that datablock
has a category element struct_mon_details.
struct_mon_detailsItem
Abstract Datatype property for struct_mon_details items.
reference_to_struct_mon_details
cross-reference to struct_mon_details
struct_mon_details.RSCC
This data item describes the specifics of the calculations that
generated the values given in attribute RSCC_all,
in category struct_mon_prot _struct_mon_prot.RSCC_main and _struct_mon_prot.RSCC_side. The
coefficients used to calculate the p(o) and p(c) maps should be
given as well as the criterion for the inclusion of map grid
points in the calculation.
The map p(o) was calculated with coefficients
2F(o) - F(c) and with phase alpha(c). F(o)
are the observed structure-factor amplitudes,
F(c) are the amplitudes calculated from the
current model and alpha(c) are the phases
calculated from the current model.
The map p(c) was calculated in program O using
a Gaussian distribution function around the
atoms in the current model.
Map grid points within 1.5 A of the
designated atoms were included in the
calculation.
The map p(o) was calculated with coefficients
F(o) and with phase alpha(c). F(o) are the
observed structure-factor amplitudes, and
alpha(c) are the phases calculated from the
current model.
The map p(c) was calculated with coefficients
F(c) and with phases alpha(c). F(c) and
alpha(c) are the structure-factor amplitudes
and phases, respectively, calculated from the
current model.
Map grid points within a van der Waals radius
of the designated atoms were included in the
calculation.
struct_mon_details.RSR
This data item describes the specifics of the calculations that
generated the values given in attribute RSR_all,
in category struct_mon_prot _struct_mon_prot.RSR_main and _struct_mon_prot.RSR_side. The
coefficients used to calculate the p(o) and p(c) maps should be
given as well as the criterion for the inclusion of map grid
points in the calculation.
The map p(o) was calculated with coefficients
2F(o) - F(c) and with phase alpha(c). F(o)
are the observed structure-factor amplitudes,
F(c) are the amplitudes calculated from the
current model and alpha(c) are the phases
calculated from the current model.
The map p(c) was calculated in program O using
a Gaussian distribution function around the
atoms in the current model.
Map grid points within 1.5 A of the
designated atoms were included in the
calculation.
The map p(o) was calculated with coefficients
F(o) and with phase alpha(c). F(o) are the
observed structure-factor amplitudes, and
alpha(c) are the phases calculated from the
current model.
The map p(c) was calculated with coefficients
F(c) and with phases alpha(c). F(c) and
alpha(c) are the structure-factor amplitudes
and phases, respectively, calculated from the
current model.
Map grid points within a van der Waals radius
of the designated atoms were included in the
calculation.
struct_mon_details.prot_cis
An ideal cis peptide bond would have an omega torsion angle of
zero. This data item gives the value in degrees by which the
observed torsion angle can differ from 0.0 and still be
considered cis.
30.0
struct_mon_details.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
struct_mon_nucl
Data items in the STRUCT_MON_NUCL category record details about
structural properties of a nucleic acid when analyzed at the
monomer level. Analogous data items for proteins are given in
the STRUCT_MON_PROT category. For items where the value of the
property depends on the method employed to calculate it,
details of the method of calculation are given using data items
in the STRUCT_MON_DETAILS category.
Example 1 - based on NDB structure BDL028.
<PDBx:struct_mon_nuclCategory>
<PDBx:struct_mon_nucl label_alt_id="A" label_asym_id="A" label_comp_id="C" label_seq_id="1">
<PDBx:alpha></PDBx:alpha>
<PDBx:beta></PDBx:beta>
<PDBx:delta>131.9</PDBx:delta>
<PDBx:epsilon>222.1</PDBx:epsilon>
<PDBx:gamma>29.9</PDBx:gamma>
<PDBx:zeta>174.2</PDBx:zeta>
</PDBx:struct_mon_nucl>
<PDBx:struct_mon_nucl label_alt_id="A" label_asym_id="A" label_comp_id="G" label_seq_id="2">
<PDBx:alpha>334.0</PDBx:alpha>
<PDBx:beta>130.6</PDBx:beta>
<PDBx:delta>125.6</PDBx:delta>
<PDBx:epsilon>167.6</PDBx:epsilon>
<PDBx:gamma>33.1</PDBx:gamma>
<PDBx:zeta>270.9</PDBx:zeta>
</PDBx:struct_mon_nucl>
<PDBx:struct_mon_nucl label_alt_id="A" label_asym_id="A" label_comp_id="T" label_seq_id="3">
<PDBx:alpha>258.2</PDBx:alpha>
<PDBx:beta>178.7</PDBx:beta>
<PDBx:delta>114.6</PDBx:delta>
<PDBx:epsilon>216.6</PDBx:epsilon>
<PDBx:gamma>101.0</PDBx:gamma>
<PDBx:zeta>259.3</PDBx:zeta>
</PDBx:struct_mon_nucl>
</PDBx:struct_mon_nuclCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
struct_mon_nuclCategory
This property indicates that datablock
has a category element struct_mon_nucl.
struct_mon_nuclItem
Abstract Datatype property for struct_mon_nucl items.
reference_to_struct_mon_nucl
cross-reference to struct_mon_nucl
struct_mon_nucl.P
P is the phase angle of pseudorotation for five-membered rings.
For ribose and deoxyribose sugars in nucleic
acids
(tau4 +tau1)-(tau3+tau0)
P = ATAN (-------------------------)
2tau2 (sin 36+sin 72)
If tau2 is <0, then P=P+180 degree (Altona & Sundaralingam,
1972).
Ref: Altona, C. & Sundaralingam, M. (1972).
J. Am. Chem. Soc. 94, 8205-8212.
struct_mon_nucl.RSCC_all
The real-space (linear) correlation coefficient RSCC, as
described by Jones et al. (1991), evaluated over all atoms in the
nucleic acid monomer.
sum|p~obs~ - <p~obs~>| * sum|p~calc~ - <p~calc~>|
RSCC = -------------------------------------------------
[ sum|p~obs~ - <p~obs~> |^2^
* sum|p~calc~ - <p~calc~>|^2^ ]^1/2^
p~obs~ = the density in an 'experimental' map
p~calc~ = the density in a 'calculated' map
sum is taken over the specified grid points
Details of how these maps were calculated should be given
in attribute RSCC in category struct_mon_details. < > indicates an average and the
sums are taken over all map grid points near the relevant atoms.
The radius for including grid points in the calculation should
also be given in attribute RSCC.
in category struct_mon_details
Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M.
(1991). Acta Cryst. A47, 110-119.
struct_mon_nucl.RSCC_base
The real-space (linear) correlation coefficient RSCC, as
described by Jones et al. (1991), evaluated over all atoms in the
base moiety of the nucleic acid monomer.
sum|p~obs~ - <p~obs~>| * sum|p~calc~ - <p~calc~>|
RSCC = -------------------------------------------------
[ sum|p~obs~ - <p~obs~> |^2^
* sum|p~calc~ - <p~calc~>|^2^ ]^1/2^
p~obs~ = the density in an 'experimental' map
p~calc~ = the density in a 'calculated' map
sum is taken over the specified grid points
Details of how these maps were calculated should be given
in attribute RSCC in category struct_mon_details. < > indicates an average and the
sums are taken over all map grid points near the relevant atoms.
The radius for including grid points in the calculation should
also be given in attribute RSCC.
in category struct_mon_details
Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M.
(1991). Acta Cryst. A47, 110-119.
struct_mon_nucl.RSCC_phos
The real-space (linear) correlation coefficient RSCC, as
described by Jones et al. (1991), evaluated over all atoms in the
phosphate moiety of the nucleic acid monomer.
sum|p~obs~ - <p~obs~>| * sum|p~calc~ - <p~calc~>|
RSCC = -------------------------------------------------
[ sum|p~obs~ - <p~obs~> |^2^
* sum|p~calc~ - <p~calc~>|^2^ ]^1/2^
p~obs~ = the density in an 'experimental' map
p~calc~ = the density in a 'calculated' map
sum is taken over the specified grid points
Details of how these maps were calculated should be given
in attribute RSCC in category struct_mon_details. < > indicates an average and the
sums are taken over all map grid points near the relevant atoms.
The radius for including grid points in the calculation should
also be given in attribute RSCC.
in category struct_mon_details
Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M.
(1991). Acta Cryst. A47, 110-119.
struct_mon_nucl.RSCC_sugar
The real-space (linear) correlation coefficient RSCC, as
described by Jones et al. (1991), evaluated over all atoms in the
sugar moiety of the nucleic acid monomer.
sum|p~obs~ - <p~obs~>| * sum|p~calc~ - <p~calc~>|
RSCC = -------------------------------------------------
[ sum|p~obs~ - <p~obs~> |^2^
* sum|p~calc~ - <p~calc~>|^2^ ]^1/2^
p~obs~ = the density in an 'experimental' map
p~calc~ = the density in a 'calculated' map
sum is taken over the specified grid points
Details of how these maps were calculated should be given
in attribute RSCC in category struct_mon_details. < > indicates an average and the
sums are taken over all map grid points near the relevant atoms.
The radius for including grid points in the calculation should
also be given in attribute RSCC.
in category struct_mon_details
Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M.
(1991). Acta Cryst. A47, 110-119.
struct_mon_nucl.RSR_all
The real-space residual RSR, as described by Branden & Jones
(1990), evaluated over all atoms in the nucleic acid monomer.
sum|p~obs~ - p~calc~|
RSR = ---------------------
sum|p~obs~ + p~calc~|
p~obs~ = the density in an 'experimental' map
p~calc~ = the density in a 'calculated' map
sum is taken over the specified grid points
Details of how these maps were calculated should be given
in attribute RSR in category struct_mon_details. The sums are taken over all map grid
points near the relevant atoms. The radius for including grid
points in the calculation should also be given in
attribute RSR.
in category struct_mon_details
Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343,
687-689.
struct_mon_nucl.RSR_base
The real-space residual RSR, as described by Branden & Jones
(1990), evaluated over all atoms in the base moiety of the
nucleic acid monomer.
sum|p~obs~ - p~calc~|
RSR = ---------------------
sum|p~obs~ + p~calc~|
p~obs~ = the density in an 'experimental' map
p~calc~ = the density in a 'calculated' map
sum is taken over the specified grid points
Details of how these maps were calculated should be given
in attribute RSR in category struct_mon_details. The sums are taken over all map grid
points near the relevant atoms. The radius for including grid
points in the calculation should also be given in
attribute RSR.
in category struct_mon_details
Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343,
687-689.
struct_mon_nucl.RSR_phos
The real-space residual RSR, as described by Branden & Jones
(1990), evaluated over all atoms in the phosphate moiety of the
nucleic acid monomer.
sum|p~obs~ - p~calc~|
RSR = ---------------------
sum|p~obs~ + p~calc~|
p~obs~ = the density in an 'experimental' map
p~calc~ = the density in a 'calculated' map
sum is taken over the specified grid points
Details of how these maps were calculated should be given
in attribute RSR in category struct_mon_details. The sums are taken over all map grid
points near the relevant atoms. The radius for including grid
points in the calculation should also be given in
attribute RSR.
in category struct_mon_details
Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343,
687-689.
struct_mon_nucl.RSR_sugar
The real-space residual RSR, as described by Branden & Jones
(1990), evaluated over all atoms in the sugar moiety of the
nucleic acid monomer.
sum|p~obs~ - p~calc~|
RSR = ---------------------
sum|p~obs~ + p~calc~|
p~obs~ = the density in an 'experimental' map
p~calc~ = the density in a 'calculated' map
sum is taken over the specified grid points
Details of how these maps were calculated should be given
in attribute RSR in category struct_mon_details. The sums are taken over all map grid
points near the relevant atoms. The radius for including grid
points in the calculation should also be given in
attribute RSR.
in category struct_mon_details
Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343,
687-689.
struct_mon_nucl.alpha
The value in degrees of the backbone torsion angle alpha
(O3'-P-O5'-C5').
struct_mon_nucl.auth_asym_id
A component of the identifier for participants in the site.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
struct_mon_nucl.auth_comp_id
A component of the identifier for participants in the site.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
struct_mon_nucl.auth_seq_id
A component of the identifier for participants in the site.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
struct_mon_nucl.beta
The value in degrees of the backbone torsion angle beta
(P-O5'-C5'-C4').
struct_mon_nucl.chi1
The value in degrees of the sugar-base torsion angle chi1
(O4'-C1'-N1-C2).
struct_mon_nucl.chi2
The value in degrees of the sugar-base torsion angle chi2
(O4'-C1'-N9-C4).
struct_mon_nucl.delta
The value in degrees of the backbone torsion angle delta
(C5'-C4'-C3'-O3').
struct_mon_nucl.details
A description of special aspects of the residue, its
conformation, behaviour in refinement, or any other aspect
that requires annotation.
Part of the phosphodiester backbone not in
density.
struct_mon_nucl.epsilon
The value in degrees of the backbone torsion angle epsilon
(C4'-C3'-O3'-P).
struct_mon_nucl.gamma
The value in degrees of the backbone torsion angle gamma
(O5'-C5'-C4'-C3').
struct_mon_nucl.mean_B_all
The mean value of the isotropic displacement parameter
for all atoms in the monomer.
struct_mon_nucl.mean_B_base
The mean value of the isotropic displacement parameter
for atoms in the base moiety of the nucleic acid monomer.
struct_mon_nucl.mean_B_phos
The mean value of the isotropic displacement parameter
for atoms in the phosphate moiety of the nucleic acid monomer.
struct_mon_nucl.mean_B_sugar
The mean value of the isotropic displacement parameter
for atoms in the sugar moiety of the nucleic acid monomer.
struct_mon_nucl.nu0
The value in degrees of the sugar torsion angle nu0
(C4'-O4'-C1'-C2').
struct_mon_nucl.nu1
The value in degrees of the sugar torsion angle nu1
(O4'-C1'-C2'-C3').
struct_mon_nucl.nu2
The value in degrees of the sugar torsion angle nu2
(C1'-C2'-C3'-C4').
struct_mon_nucl.nu3
The value in degrees of the sugar torsion angle nu3
(C2'-C3'-C4'-O4').
struct_mon_nucl.nu4
The value in degrees of the sugar torsion angle nu4
(C3'-C4'-O4'-C1').
struct_mon_nucl.tau0
The value in degrees of the sugar torsion angle tau0
(C4'-O4'-C1'-C2').
struct_mon_nucl.tau1
The value in degrees of the sugar torsion angle tau1
(O4'-C1'-C2'-C3').
struct_mon_nucl.tau2
The value in degrees of the sugar torsion angle tau2
(C1'-C2'-C3'-C4').
struct_mon_nucl.tau3
The value in degrees of the sugar torsion angle tau3
(C2'-C3'-C4'-O4').
struct_mon_nucl.tau4
The value in degrees of the sugar torsion angle tau4
(C3'-C4'-O4'-C1').
struct_mon_nucl.taum
The maximum amplitude of puckering. This is derived from the
pseudorotation value P and the torsion angles in the ribose
ring.
Tau2= Taum cosP
Tau3= Taum cos(P+144)
Tau4= Taum cos(P+288)
Tau0= Taum cos(P+ 72)
Tau1= Taum cos(P+216)
struct_mon_nucl.zeta
The value in degrees of the backbone torsion angle zeta
(C3'-O3'-P-O5').
struct_mon_nucl.label_alt_id
A component of the identifier for participants in the site.
This data item is a pointer to attribute id in category atom_sites_alt in the
ATOM_SITES_ALT category.
struct_mon_nucl.label_asym_id
A component of the identifier for participants in the site.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
struct_mon_nucl.label_comp_id
A component of the identifier for participants in the site.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
struct_mon_nucl.label_seq_id
A component of the identifier for participants in the site.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
struct_mon_prot
Data items in the STRUCT_MON_PROT category record details about
structural properties of a protein when analyzed at the monomer
level. Analogous data items for nucleic acids are given in the
STRUCT_MON_NUCL category. For items where the value of the
property depends on the method employed to calculate it,
details of the method of calculation are given using data items
in the STRUCT_MON_DETAILS category.
Example 1 - based on laboratory records for protein NS1.
This example provides details for residue ARG 35.
<PDBx:struct_mon_protCategory>
<PDBx:struct_mon_prot label_alt_id="A" label_asym_id="A" label_comp_id="ARG" label_seq_id="35">
<PDBx:RSCC_all>0.90</PDBx:RSCC_all>
<PDBx:RSR_all>0.18</PDBx:RSR_all>
<PDBx:chi1>-67.9</PDBx:chi1>
<PDBx:chi2>-174.7</PDBx:chi2>
<PDBx:chi3>-67.7</PDBx:chi3>
<PDBx:chi4>-86.3</PDBx:chi4>
<PDBx:chi5>4.2</PDBx:chi5>
<PDBx:mean_B_all>30.0</PDBx:mean_B_all>
<PDBx:mean_B_main>25.0</PDBx:mean_B_main>
<PDBx:mean_B_side>35.1</PDBx:mean_B_side>
<PDBx:omega>180.1</PDBx:omega>
<PDBx:phi>-60.3</PDBx:phi>
<PDBx:psi>-46.0</PDBx:psi>
</PDBx:struct_mon_prot>
</PDBx:struct_mon_protCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
struct_mon_protCategory
This property indicates that datablock
has a category element struct_mon_prot.
struct_mon_protItem
Abstract Datatype property for struct_mon_prot items.
reference_to_struct_mon_prot
cross-reference to struct_mon_prot
struct_mon_prot.RSCC_all
The real-space (linear) correlation coefficient RSCC, as
described by Jones et al. (1991), evaluated over all atoms
in the monomer.
sum|p~obs~ - <p~obs~>| * sum|p~calc~ - <p~calc~>|
RSCC = -------------------------------------------------
[ sum|p~obs~ - <p~obs~> |^2^
* sum|p~calc~ - <p~calc~>|^2^ ]^1/2^
p~obs~ = the density in an 'experimental' map
p~calc~ = the density in a 'calculated' map
sum is taken over the specified grid points
Details of how these maps were calculated should be given
in attribute RSCC in category struct_mon_details. < > indicates an average and the
sums are taken over all map grid points near the relevant atoms.
The radius for including grid points in the calculation should
also be given in attribute RSCC.
in category struct_mon_details
Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M.
(1991). Acta Cryst. A47, 110-119.
struct_mon_prot.RSCC_main
The real-space (linear) correlation coefficient RSCC, as
described by Jones et al. (1991), evaluated over all atoms
in the main chain of the monomer.
sum|p~obs~ - <p~obs~>| * sum|p~calc~ - <p~calc~>|
RSCC = -------------------------------------------------
[ sum|p~obs~ - <p~obs~> |^2^
* sum|p~calc~ - <p~calc~>|^2^ ]^1/2^
p~obs~ = the density in an 'experimental' map
p~calc~ = the density in a 'calculated' map
sum is taken over the specified grid points
Details of how these maps were calculated should be given
in attribute RSCC in category struct_mon_details. < > indicates an average and the
sums are taken over all map grid points near the relevant atoms.
The radius for including grid points in the calculation should
also be given in attribute RSCC.
in category struct_mon_details
Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M.
(1991). Acta Cryst. A47, 110-119.
struct_mon_prot.RSCC_side
The real-space (linear) correlation coefficient RSCC, as
described by Jones et al. (1991), evaluated over all atoms
in the side chain of the monomer.
sum|p~obs~ - <p~obs~>| * sum|p~calc~ - <p~calc~>|
RSCC = -------------------------------------------------
[ sum|p~obs~ - <p~obs~> |^2^
* sum|p~calc~ - <p~calc~>|^2^ ]^1/2^
p~obs~ = the density in an 'experimental' map
p~calc~ = the density in a 'calculated' map
sum is taken over the specified grid points
Details of how these maps were calculated should be given
in attribute RSCC in category struct_mon_details. < > indicates an average and the
sums are taken over all map grid points near the relevant atoms.
The radius for including grid points in the calculation should
also be given in attribute RSCC.
in category struct_mon_details
Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M.
(1991). Acta Cryst. A47, 110-119.
struct_mon_prot.RSR_all
The real-space residual RSR, as described by Branden & Jones
(1990), evaluated over all atoms in the monomer.
sum|p~obs~ - p~calc~|
RSR = ---------------------
sum|p~obs~ + p~calc~|
p~obs~ = the density in an 'experimental' map
p~calc~ = the density in a 'calculated' map
sum is taken over the specified grid points
Details of how these maps were calculated should be given
in attribute RSR in category struct_mon_details. The sums are taken over all map grid
points near the relevant atoms. The radius for including grid
points in the calculation should also be given in
attribute RSR.
in category struct_mon_details
Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343,
687-689.
struct_mon_prot.RSR_main
The real-space residual RSR, as described by Branden & Jones
(1990), evaluated over all atoms in the main chain of the
monomer.
sum|p~obs~ - p~calc~|
RSR = ---------------------
sum|p~obs~ + p~calc~|
p~obs~ = the density in an 'experimental' map
p~calc~ = the density in a 'calculated' map
sum is taken over the specified grid points
Details of how these maps were calculated should be given
in attribute RSR in category struct_mon_details. The sums are taken over all map grid
points near the relevant atoms. The radius for including grid
points in the calculation should also be given in
attribute RSR.
in category struct_mon_details
Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343,
687-689.
struct_mon_prot.RSR_side
The real-space residual RSR, as described by Branden & Jones
(1990), evaluated over all atoms in the side chain of the
monomer.
sum|p~obs~ - p~calc~|
RSR = ---------------------
sum|p~obs~ + p~calc~|
p~obs~ = the density in an 'experimental' map
p~calc~ = the density in a 'calculated' map
sum is taken over the specified grid points
Details of how these maps were calculated should be given
in attribute RSR in category struct_mon_details. The sums are taken over all map grid
points near the relevant atoms. The radius for including grid
points in the calculation should also be given in
attribute RSR.
in category struct_mon_details
Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343,
687-689.
struct_mon_prot.auth_asym_id
A component of the identifier for the monomer.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
struct_mon_prot.auth_comp_id
A component of the identifier for the monomer.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
struct_mon_prot.auth_seq_id
A component of the identifier for the monomer.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
struct_mon_prot.chi1
The value in degrees of the side-chain torsion angle chi1, for
those residues containing such an angle.
struct_mon_prot.chi2
The value in degrees of the side-chain torsion angle chi2, for
those residues containing such an angle.
struct_mon_prot.chi3
The value in degrees of the side-chain torsion angle chi3, for
those residues containing such an angle.
struct_mon_prot.chi4
The value in degrees of the side-chain torsion angle chi4, for
those residues containing such an angle.
struct_mon_prot.chi5
The value in degrees of the side-chain torsion angle chi5, for
those residues containing such an angle.
struct_mon_prot.details
A description of special aspects of the residue, its
conformation, behaviour in refinement, or any other aspect that
requires annotation.
very poor density
The side chain of this density may occupy
alternative conformations, but alternative
conformations were not fit in this model.
This residue has a close contact with the
bound inhibitor, which may account for
the nonstandard conformation of the side
chain.
struct_mon_prot.mean_B_all
The mean value of the isotropic displacement parameter for all
atoms in the monomer.
struct_mon_prot.mean_B_main
The mean value of the isotropic displacement parameter for atoms
in the main chain of the monomer.
struct_mon_prot.mean_B_side
The mean value of the isotropic displacement parameter for atoms
in the side chain of the monomer.
struct_mon_prot.omega
The value in degrees of the main-chain torsion angle omega.
struct_mon_prot.phi
The value in degrees of the main-chain torsion angle phi.
struct_mon_prot.psi
The value in degrees of the main-chain torsion angle psi.
struct_mon_prot.label_alt_id
A component of the identifier for the monomer.
This data item is a pointer to attribute id in category atom_sites_alt in the
ATOM_SITES_ALT category.
struct_mon_prot.label_asym_id
A component of the identifier for the monomer.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
struct_mon_prot.label_comp_id
A component of the identifier for the monomer.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
struct_mon_prot.label_seq_id
A component of the identifier for the monomer.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
struct_mon_prot_cis
Data items in the STRUCT_MON_PROT_CIS category identify
monomers that have been found to have the peptide bond in the cis
conformation. The criterion used to select residues to be
designated as containing cis peptide bonds is given in
attribute prot_cis in category struct_mon_details.
Example 1 - based on PDB structure 1ACY of Ghiara, Stura, Stanfield,
Profy & Wilson [Science (1994), 264, 82-85].
<PDBx:struct_mon_prot_cisCategory>
<PDBx:struct_mon_prot_cis pdbx_id="1">
<PDBx:label_alt_id></PDBx:label_alt_id>
<PDBx:label_asym_id>L</PDBx:label_asym_id>
<PDBx:label_comp_id>PRO</PDBx:label_comp_id>
<PDBx:label_seq_id>8</PDBx:label_seq_id>
<PDBx:pdbx_PDB_model_num>1</PDBx:pdbx_PDB_model_num>
</PDBx:struct_mon_prot_cis>
<PDBx:struct_mon_prot_cis pdbx_id="2">
<PDBx:label_alt_id></PDBx:label_alt_id>
<PDBx:label_asym_id>L</PDBx:label_asym_id>
<PDBx:label_comp_id>PRO</PDBx:label_comp_id>
<PDBx:label_seq_id>77</PDBx:label_seq_id>
<PDBx:pdbx_PDB_model_num>1</PDBx:pdbx_PDB_model_num>
</PDBx:struct_mon_prot_cis>
<PDBx:struct_mon_prot_cis pdbx_id="3">
<PDBx:label_alt_id></PDBx:label_alt_id>
<PDBx:label_asym_id>L</PDBx:label_asym_id>
<PDBx:label_comp_id>PRO</PDBx:label_comp_id>
<PDBx:label_seq_id>95</PDBx:label_seq_id>
<PDBx:pdbx_PDB_model_num>1</PDBx:pdbx_PDB_model_num>
</PDBx:struct_mon_prot_cis>
<PDBx:struct_mon_prot_cis pdbx_id="4">
<PDBx:label_alt_id></PDBx:label_alt_id>
<PDBx:label_asym_id>L</PDBx:label_asym_id>
<PDBx:label_comp_id>PRO</PDBx:label_comp_id>
<PDBx:label_seq_id>141</PDBx:label_seq_id>
<PDBx:pdbx_PDB_model_num>1</PDBx:pdbx_PDB_model_num>
</PDBx:struct_mon_prot_cis>
</PDBx:struct_mon_prot_cisCategory>
0
1
0
1
0
1
1
1
1
1
1
1
1
1
0
1
0
1
1
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
struct_mon_prot_cisCategory
This property indicates that datablock
has a category element struct_mon_prot_cis.
struct_mon_prot_cisItem
Abstract Datatype property for struct_mon_prot_cis items.
reference_to_struct_mon_prot_cis
cross-reference to struct_mon_prot_cis
struct_mon_prot_cis.auth_asym_id
A component of the identifier for the monomer.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
struct_mon_prot_cis.auth_comp_id
A component of the identifier for the monomer.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
struct_mon_prot_cis.auth_seq_id
A component of the identifier for the monomer.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
struct_mon_prot_cis.label_alt_id
A component of the identifier for the monomer.
This data item is a pointer to attribute id in category atom_sites_alt in the
ATOM_SITES_ALT category.
struct_mon_prot_cis.label_asym_id
A component of the identifier for the monomer.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
struct_mon_prot_cis.label_comp_id
A component of the identifier for the monomer.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
struct_mon_prot_cis.label_seq_id
A component of the identifier for the monomer.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
struct_mon_prot_cis.pdbx_PDB_ins_code
Pointer to attribute pdbx_PDB_ins_code in category atom_site
struct_mon_prot_cis.pdbx_PDB_ins_code_2
Pointer to attribute pdbx_PDB_ins_code in category atom_site
struct_mon_prot_cis.pdbx_PDB_model_num
Pointer to attribute pdbx_PDB_model_num in category atom_site
struct_mon_prot_cis.pdbx_auth_asym_id_2
Pointer to attribute auth_asym_id in category atom_site.
struct_mon_prot_cis.pdbx_auth_comp_id_2
Pointer to attribute auth_comp_id in category atom_site.
struct_mon_prot_cis.pdbx_auth_seq_id_2
Pointer to attribute auth_seq_id in category atom_site
struct_mon_prot_cis.pdbx_label_asym_id_2
Pointer to attribute label_asym_id in category atom_site.
struct_mon_prot_cis.pdbx_label_comp_id_2
Pointer to attribute label_comp_id in category atom_site.
struct_mon_prot_cis.pdbx_label_seq_id_2
Pointer to attribute label_seq_id in category atom_site
struct_mon_prot_cis.pdbx_omega_angle
omega torsion angle
struct_mon_prot_cis.pdbx_id
ordinal index
struct_ncs_dom
Data items in the STRUCT_NCS_DOM category record information
about the domains in an ensemble of domains related by one or
more noncrystallographic symmetry operators.
A domain need not correspond to a complete polypeptide chain;
it can be composed of one or more segments in a single chain,
or by segments from more than one chain.
Example 1 - based on laboratory records for the collagen-like
peptide, HYP-.
<PDBx:struct_ncs_domCategory>
<PDBx:struct_ncs_dom id="d1" pdbx_ens_id="1">
<PDBx:details>Chains A, B, and C</PDBx:details>
</PDBx:struct_ncs_dom>
<PDBx:struct_ncs_dom id="d2" pdbx_ens_id="1">
<PDBx:details>Chains D, E, and F</PDBx:details>
</PDBx:struct_ncs_dom>
</PDBx:struct_ncs_domCategory>
0
1
1
1
struct_ncs_domCategory
This property indicates that datablock
has a category element struct_ncs_dom.
struct_ncs_domItem
Abstract Datatype property for struct_ncs_dom items.
reference_to_struct_ncs_dom
cross-reference to struct_ncs_dom
struct_ncs_dom.details
A description of special aspects of the structural elements that
comprise a domain in an ensemble of domains related by
noncrystallographic symmetry.
The loop between residues 18 and 23 in this
domain interacts with a symmetry-related
molecule, and thus deviates significantly from
the noncrystallographic threefold.
struct_ncs_dom.id
The value of attribute id in category struct_ncs_dom must uniquely identify a
record in the STRUCT_NCS_DOM list.
Note that this item need not be a number; it can be any unique
identifier.
struct_ncs_dom.pdbx_ens_id
This is a unique identifier for a collection NCS related domains.
This references item '_struct_ncs_ens.id'.
struct_ncs_dom_lim
Data items in the STRUCT_NCS_DOM_LIM category identify the
start and end points of polypeptide chain segments
that form all or part of a domain in an ensemble of domains
related by noncrystallographic symmetry.
Example 1 - based on laboratory records for the collagen-like
peptide, HYP-.
<PDBx:struct_ncs_dom_limCategory>
<PDBx:struct_ncs_dom_lim dom_id="d1" pdbx_component_id="1" pdbx_ens_id="1">
<PDBx:beg_label_alt_id></PDBx:beg_label_alt_id>
<PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id>
<PDBx:beg_label_comp_id>PRO</PDBx:beg_label_comp_id>
<PDBx:beg_label_seq_id>1</PDBx:beg_label_seq_id>
<PDBx:end_label_alt_id></PDBx:end_label_alt_id>
<PDBx:end_label_asym_id>A</PDBx:end_label_asym_id>
<PDBx:end_label_comp_id>GLY</PDBx:end_label_comp_id>
<PDBx:end_label_seq_id>29</PDBx:end_label_seq_id>
</PDBx:struct_ncs_dom_lim>
<PDBx:struct_ncs_dom_lim dom_id="d1" pdbx_component_id="2" pdbx_ens_id="1">
<PDBx:beg_label_alt_id></PDBx:beg_label_alt_id>
<PDBx:beg_label_asym_id>B</PDBx:beg_label_asym_id>
<PDBx:beg_label_comp_id>PRO</PDBx:beg_label_comp_id>
<PDBx:beg_label_seq_id>31</PDBx:beg_label_seq_id>
<PDBx:end_label_alt_id></PDBx:end_label_alt_id>
<PDBx:end_label_asym_id>B</PDBx:end_label_asym_id>
<PDBx:end_label_comp_id>GLY</PDBx:end_label_comp_id>
<PDBx:end_label_seq_id>59</PDBx:end_label_seq_id>
</PDBx:struct_ncs_dom_lim>
<PDBx:struct_ncs_dom_lim dom_id="d1" pdbx_component_id="3" pdbx_ens_id="1">
<PDBx:beg_label_alt_id></PDBx:beg_label_alt_id>
<PDBx:beg_label_asym_id>C</PDBx:beg_label_asym_id>
<PDBx:beg_label_comp_id>PRO</PDBx:beg_label_comp_id>
<PDBx:beg_label_seq_id>61</PDBx:beg_label_seq_id>
<PDBx:end_label_alt_id></PDBx:end_label_alt_id>
<PDBx:end_label_asym_id>B</PDBx:end_label_asym_id>
<PDBx:end_label_comp_id>GLY</PDBx:end_label_comp_id>
<PDBx:end_label_seq_id>89</PDBx:end_label_seq_id>
</PDBx:struct_ncs_dom_lim>
<PDBx:struct_ncs_dom_lim dom_id="d2" pdbx_component_id="1" pdbx_ens_id="1">
<PDBx:beg_label_alt_id></PDBx:beg_label_alt_id>
<PDBx:beg_label_asym_id>D</PDBx:beg_label_asym_id>
<PDBx:beg_label_comp_id>PRO</PDBx:beg_label_comp_id>
<PDBx:beg_label_seq_id>91</PDBx:beg_label_seq_id>
<PDBx:end_label_alt_id></PDBx:end_label_alt_id>
<PDBx:end_label_asym_id>D</PDBx:end_label_asym_id>
<PDBx:end_label_comp_id>GLY</PDBx:end_label_comp_id>
<PDBx:end_label_seq_id>119</PDBx:end_label_seq_id>
</PDBx:struct_ncs_dom_lim>
<PDBx:struct_ncs_dom_lim dom_id="d2" pdbx_component_id="2" pdbx_ens_id="1">
<PDBx:beg_label_alt_id></PDBx:beg_label_alt_id>
<PDBx:beg_label_asym_id>E</PDBx:beg_label_asym_id>
<PDBx:beg_label_comp_id>PRO</PDBx:beg_label_comp_id>
<PDBx:beg_label_seq_id>121</PDBx:beg_label_seq_id>
<PDBx:end_label_alt_id></PDBx:end_label_alt_id>
<PDBx:end_label_asym_id>E</PDBx:end_label_asym_id>
<PDBx:end_label_comp_id>GLY</PDBx:end_label_comp_id>
<PDBx:end_label_seq_id>149</PDBx:end_label_seq_id>
</PDBx:struct_ncs_dom_lim>
<PDBx:struct_ncs_dom_lim dom_id="d2" pdbx_component_id="3" pdbx_ens_id="1">
<PDBx:beg_label_alt_id></PDBx:beg_label_alt_id>
<PDBx:beg_label_asym_id>F</PDBx:beg_label_asym_id>
<PDBx:beg_label_comp_id>PRO</PDBx:beg_label_comp_id>
<PDBx:beg_label_seq_id>151</PDBx:beg_label_seq_id>
<PDBx:end_label_alt_id></PDBx:end_label_alt_id>
<PDBx:end_label_asym_id>F</PDBx:end_label_asym_id>
<PDBx:end_label_comp_id>GLY</PDBx:end_label_comp_id>
<PDBx:end_label_seq_id>179</PDBx:end_label_seq_id>
</PDBx:struct_ncs_dom_lim>
</PDBx:struct_ncs_dom_limCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
struct_ncs_dom_limCategory
This property indicates that datablock
has a category element struct_ncs_dom_lim.
struct_ncs_dom_limItem
Abstract Datatype property for struct_ncs_dom_lim items.
reference_to_struct_ncs_dom_lim
cross-reference to struct_ncs_dom_lim
struct_ncs_dom_lim.beg_auth_asym_id
A component of the identifier for the monomer at which this
segment of the domain begins.
struct_ncs_dom_lim.beg_auth_comp_id
A component of the identifier for the monomer at which this
segment of the domain begins.
struct_ncs_dom_lim.beg_auth_seq_id
A component of the identifier for the monomer at which this
segment of the domain begins.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
struct_ncs_dom_lim.beg_label_alt_id
A component of the identifier for the monomer at which this
segment of the domain begins.
struct_ncs_dom_lim.beg_label_asym_id
A component of the identifier for the monomer at which this
segment of the domain begins.
This data item is a pointer to attribute id in category struct_asym in the
STRUCT_ASYM category.
struct_ncs_dom_lim.beg_label_comp_id
A component of the identifier for the monomer at which this
segment of the domain begins.
struct_ncs_dom_lim.beg_label_seq_id
A component of the identifier for the monomer at which this
segment of the domain begins.
struct_ncs_dom_lim.end_auth_asym_id
A component of the identifier for the monomer at which this
segment of the domain ends.
struct_ncs_dom_lim.end_auth_comp_id
A component of the identifier for the monomer at which this
segment of the domain ends.
struct_ncs_dom_lim.end_auth_seq_id
A component of the identifier for the monomer at which this
segment of the domain ends.
struct_ncs_dom_lim.end_label_alt_id
A component of the identifier for the monomer at which this
segment of the domain ends.
struct_ncs_dom_lim.end_label_asym_id
A component of the identifier for the monomer at which this
segment of the domain ends.
This data item is a pointer to attribute id in category struct_asym in the
STRUCT_ASYM category.
struct_ncs_dom_lim.end_label_comp_id
A component of the identifier for the monomer at which this
segment of the domain ends.
struct_ncs_dom_lim.end_label_seq_id
A component of the identifier for the monomer at which this
segment of the domain ends.
struct_ncs_dom_lim.pdbx_refine_code
record the refinement code number (from CCP4.)
struct_ncs_dom_lim.selection_details
A text description of the selection of residues that
correspond to this domain.
struct_ncs_dom_lim.dom_id
This data item is a pointer to attribute id in category struct_ncs_dom in the
STRUCT_NCS_DOM category.
struct_ncs_dom_lim.pdbx_component_id
Record number of the NCS domain limit assignment.
struct_ncs_dom_lim.pdbx_ens_id
This is a unique identifier for a collection NCS related domains.
This references item '_struct_ncs_dom.pdbx_ens_id'.
struct_ncs_ens
Data items in the STRUCT_NCS_ENS category record information
about ensembles of domains related by noncrystallographic
symmetry. The point group of the ensemble when taken as a
whole may be specified, as well as any special aspects of the
ensemble that require description.
Example 1 - based on laboratory records for the collagen-like
peptide, HYP-.
<PDBx:struct_ncs_ensCategory>
<PDBx:struct_ncs_ens id="en1">
<PDBx:details> The ensemble represents the pseudo-twofold symmetry
between domains d1 and d2.</PDBx:details>
</PDBx:struct_ncs_ens>
</PDBx:struct_ncs_ensCategory>
0
1
0
1
1
struct_ncs_ensCategory
This property indicates that datablock
has a category element struct_ncs_ens.
struct_ncs_ensItem
Abstract Datatype property for struct_ncs_ens items.
reference_to_struct_ncs_ens
cross-reference to struct_ncs_ens
struct_ncs_ens.details
A description of special aspects of the ensemble.
The ensemble has a slight translation between
domains 1 and 4, but overall it can accurately
be described as point group 222
struct_ncs_ens.point_group
The point group of the ensemble of structural elements related by
one or more noncrystallographic symmetry operations. The
relationships need not be precise; this data item is intended
to give a rough description of the noncrystallographic symmetry
relationships.
3
422
non-proper
struct_ncs_ens.id
The value of attribute id in category struct_ncs_ens must uniquely identify a
record in the STRUCT_NCS_ENS list.
Note that this item need not be a number; it can be any unique
identifier.
struct_ncs_ens_gen
Data items in the STRUCT_NCS_ENS_GEN category list domains
related by a noncrystallographic symmetry operation and
identify the operator.
Example 1 - based on laboratory records for the collagen-like
peptide, HYP-.
<PDBx:struct_ncs_ens_genCategory>
<PDBx:struct_ncs_ens_gen dom_id_1="d1" dom_id_2="d2" ens_id="en1" oper_id="ncsop1"></PDBx:struct_ncs_ens_gen>
</PDBx:struct_ncs_ens_genCategory>
1
1
1
1
struct_ncs_ens_genCategory
This property indicates that datablock
has a category element struct_ncs_ens_gen.
struct_ncs_ens_genItem
Abstract Datatype property for struct_ncs_ens_gen items.
reference_to_struct_ncs_ens_gen
cross-reference to struct_ncs_ens_gen
struct_ncs_ens_gen.dom_id_1
The identifier for the domain that will remain unchanged by the
transformation operator.
This data item is a pointer to attribute id in category struct_ncs_dom in the
STRUCT_NCS_DOM category.
struct_ncs_ens_gen.dom_id_2
The identifier for the domain that will be transformed by
application of the transformation operator.
This data item is a pointer to attribute id in category struct_ncs_dom in the
STRUCT_NCS_DOM category.
struct_ncs_ens_gen.ens_id
This data item is a pointer to attribute id in category struct_ncs_ens in the
STRUCT_NCS_ENS category.
struct_ncs_ens_gen.oper_id
This data item is a pointer to attribute id in category struct_ncs_oper in the
STRUCT_NCS_OPER category.
struct_ncs_oper
Data items in the STRUCT_NCS_OPER category describe the
noncrystallographic symmetry operations.
Each operator is specified as a matrix and a subsequent
translation vector. Operators need not represent proper
rotations.
Example 1 - based on laboratory records for the protein NS1.
<PDBx:struct_ncs_operCategory>
<PDBx:struct_ncs_oper id="ncsop1">
<PDBx:code>given</PDBx:code>
<PDBx:details> Matrix and translation vector for pseudo-twofold operation.</PDBx:details>
<PDBx:matrix11>0.247</PDBx:matrix11>
<PDBx:matrix12>0.935</PDBx:matrix12>
<PDBx:matrix13>0.256</PDBx:matrix13>
<PDBx:matrix21>0.929</PDBx:matrix21>
<PDBx:matrix22>0.153</PDBx:matrix22>
<PDBx:matrix23>0.337</PDBx:matrix23>
<PDBx:matrix31>0.276</PDBx:matrix31>
<PDBx:matrix32>0.321</PDBx:matrix32>
<PDBx:matrix33>-0.906</PDBx:matrix33>
<PDBx:vector1>-8.253</PDBx:vector1>
<PDBx:vector2>-11.743</PDBx:vector2>
<PDBx:vector3>-1.782</PDBx:vector3>
</PDBx:struct_ncs_oper>
</PDBx:struct_ncs_operCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
struct_ncs_operCategory
This property indicates that datablock
has a category element struct_ncs_oper.
struct_ncs_operItem
Abstract Datatype property for struct_ncs_oper items.
reference_to_struct_ncs_oper
cross-reference to struct_ncs_oper
given
generate
A code to indicate whether this operator describes a
relationship between coordinates all of which are given in the
data block (in which case the value of code is 'given'), or
whether the operator is used to generate new coordinates from
those that are given in the data block (in which case the value
of code is 'generate').
struct_ncs_oper.details
A description of special aspects of the noncrystallographic
symmetry operator.
The operation is given as a precise threefold
rotation, despite the fact the best rms
fit between domain 1 and domain 2 yields a
rotation of 119.7 degrees and a translation
of 0.13 angstroms.
struct_ncs_oper.matrix11
The [1][1] element of the 3x3 matrix component of a
noncrystallographic symmetry operation.
struct_ncs_oper.matrix12
The [1][2] element of the 3x3 matrix component of a
noncrystallographic symmetry operation.
struct_ncs_oper.matrix13
The [1][3] element of the 3x3 matrix component of a
noncrystallographic symmetry operation.
struct_ncs_oper.matrix21
The [2][1] element of the 3x3 matrix component of a
noncrystallographic symmetry operation.
struct_ncs_oper.matrix22
The [2][2] element of the 3x3 matrix component of a
noncrystallographic symmetry operation.
struct_ncs_oper.matrix23
The [2][3] element of the 3x3 matrix component of a
noncrystallographic symmetry operation.
struct_ncs_oper.matrix31
The [3][1] element of the 3x3 matrix component of a
noncrystallographic symmetry operation.
struct_ncs_oper.matrix32
The [3][2] element of the 3x3 matrix component of a
noncrystallographic symmetry operation.
struct_ncs_oper.matrix33
The [3][3] element of the 3x3 matrix component of a
noncrystallographic symmetry operation.
struct_ncs_oper.vector1
The [1] element of the three-element vector component of a
noncrystallographic symmetry operation.
struct_ncs_oper.vector2
The [2] element of the three-element vector component of a
noncrystallographic symmetry operation.
struct_ncs_oper.vector3
The [3] element of the three-element vector component of a
noncrystallographic symmetry operation.
struct_ncs_oper.id
The value of attribute id in category struct_ncs_oper must uniquely identify a
record in the STRUCT_NCS_OPER list.
Note that this item need not be a number; it can be any unique
identifier.
struct_ref
Data items in the STRUCT_REF category allow the author of a
data block to relate the entities or biological units
described in the data block to information archived in external
databases.
For references to the sequence of a polymer, the value of
the data item attribute seq_align in category struct_ref is used to indicate
whether the correspondence between the sequence of the entity
or biological unit in the data block and the sequence in the
referenced database entry is 'complete' or 'partial'. If
this value is 'partial', the region (or regions) of the
alignment may be delimited using data items in the
STRUCT_REF_SEQ category.
Similarly, the value of attribute seq_dif in category struct_ref is used to indicate
whether the two sequences contain point differences. If the
value is 'yes', the differences may be identified and annotated
using data items in the STRUCT_REF_SEQ_DIF category.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:struct_refCategory>
<PDBx:struct_ref id="1">
<PDBx:biol_id></PDBx:biol_id>
<PDBx:db_code>12345</PDBx:db_code>
<PDBx:db_name>Genbank</PDBx:db_name>
<PDBx:details></PDBx:details>
<PDBx:entity_id>1</PDBx:entity_id>
<PDBx:seq_align>entire</PDBx:seq_align>
<PDBx:seq_dif>yes</PDBx:seq_dif>
</PDBx:struct_ref>
<PDBx:struct_ref id="2">
<PDBx:biol_id>2</PDBx:biol_id>
<PDBx:db_code>1ABC</PDBx:db_code>
<PDBx:db_name>PDB</PDBx:db_name>
<PDBx:details> The structure of the closely related compound,
isobutyryl-pepstatin (pepstatin A) in complex with
rhizopuspepsin</PDBx:details>
<PDBx:entity_id></PDBx:entity_id>
<PDBx:seq_align></PDBx:seq_align>
<PDBx:seq_dif></PDBx:seq_dif>
</PDBx:struct_ref>
</PDBx:struct_refCategory>
0
1
1
1
1
1
0
1
1
1
0
1
0
1
0
1
0
1
0
1
1
struct_refCategory
This property indicates that datablock
has a category element struct_ref.
struct_refItem
Abstract Datatype property for struct_ref items.
reference_to_struct_ref
cross-reference to struct_ref
struct_ref.biol_id
This data item is a pointer to attribute id in category struct_biol in the
STRUCT_BIOL category.
struct_ref.db_code
The code for this entity or biological unit or for a closely
related entity or biological unit in the named database.
1ABC
ABCDEF
struct_ref.db_name
The name of the database containing reference information about
this entity or biological unit.
PDB
CSD
Genbank
struct_ref.details
A description of special aspects of the relationship between
the entity or biological unit described in the data block and
that in the referenced database entry.
struct_ref.entity_id
This data item is a pointer to attribute id in category entity in the ENTITY category.
struct_ref.pdbx_align_begin
Beginning index in the chemical sequence from the
reference database.
1
2
struct_ref.pdbx_db_accession
Accession code of the reference database.
P07617
struct_ref.pdbx_seq_one_letter_code
Database chemical sequence expressed as string of one-letter
amino acid codes.
A for alanine or adenine
B for ambiguous asparagine/aspartic-acid
R for arginine
N for asparagine
D for aspartic-acid
C for cysteine or cystine or cytosine
Q for glutamine
E for glutamic-acid
Z for ambiguous glutamine/glutamic acid
G for glycine or guanine
H for histidine
I for isoleucine
L for leucine
K for lysine
M for methionine
F for phenylalanine
P for proline
S for serine
T for threonine or thymine
W for tryptophan
Y for tyrosine
V for valine
U for uracil
O for water
X for other
complete
partial
A flag to indicate the scope of the alignment between the
sequence of the entity or biological unit described in the data
block and that in the referenced database entry. 'entire'
indicates that alignment spans the entire length of both
sequences (although point differences may occur and can be
annotated using the data items in the STRUCT_REF_SEQ_DIF
category). 'partial' indicates a partial alignment. The region
(or regions) of the alignment may be delimited using data items
in the STRUCT_REF_SEQ category. This data item may also take
the value '.', indicating that the reference is not to a
sequence.
no
n
yes
y
A flag to indicate the presence ('yes') or absence ('no') of
point differences between the sequence of the entity or
biological unit described in the data block and that in
the referenced database entry. This data item may also
take the value '.', indicating that the reference is not to a
sequence.
struct_ref.id
The value of attribute id in category struct_ref must uniquely identify a record
in the STRUCT_REF list.
Note that this item need not be a number; it can be any unique
identifier.
struct_ref_seq
Data items in the STRUCT_REF_SEQ category provide a mechanism
for indicating and annotating a region (or regions) of alignment
between the sequence of an entity or biological unit described
in the data block and the sequence in the referenced database
entry.
Example 1 - based on the sequence alignment of CHER from M. xantus
(36 to 288) and CHER from S. typhimurium (18 to 276).
<PDBx:struct_ref_seqCategory>
<PDBx:struct_ref_seq align_id="alg1">
<PDBx:db_align_beg>18</PDBx:db_align_beg>
<PDBx:db_align_end>276</PDBx:db_align_end>
<PDBx:details> The alignment contains 3 gaps larger than 2 residues</PDBx:details>
<PDBx:ref_id>seqdb1</PDBx:ref_id>
<PDBx:seq_align_beg>36</PDBx:seq_align_beg>
<PDBx:seq_align_end>288</PDBx:seq_align_end>
</PDBx:struct_ref_seq>
</PDBx:struct_ref_seqCategory>
1
1
1
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
1
1
1
struct_ref_seqCategory
This property indicates that datablock
has a category element struct_ref_seq.
struct_ref_seqItem
Abstract Datatype property for struct_ref_seq items.
reference_to_struct_ref_seq
cross-reference to struct_ref_seq
struct_ref_seq.db_align_beg
The sequence position in the referenced database entry
at which the alignment begins.
struct_ref_seq.db_align_end
The sequence position in the referenced database entry
at which the alignment ends.
struct_ref_seq.details
A description of special aspects of the sequence alignment.
struct_ref_seq.pdbx_PDB_id_code
The PDB code of the structure.
1BBP
struct_ref_seq.pdbx_auth_seq_align_beg
Initial position in the PDB sequence segment.
1
2
struct_ref_seq.pdbx_auth_seq_align_end
Ending position in the PDB sequence segment
1
2
struct_ref_seq.pdbx_db_accession
Accession code of the reference database.
P07617
struct_ref_seq.pdbx_db_align_beg_ins_code
Initial insertion code of the sequence segment of the
reference database.
1
2
struct_ref_seq.pdbx_db_align_end_ins_code
Ending insertion code of the sequence segment of the
reference database.
1
2
struct_ref_seq.pdbx_seq_align_beg_ins_code
Initial insertion code of the PDB sequence segment.
1
2
struct_ref_seq.pdbx_seq_align_end_ins_code
Ending insertion code of the sequence segment
1
2
struct_ref_seq.pdbx_strand_id
The PDB strand/chain ID .
A
B
struct_ref_seq.ref_id
This data item is a pointer to attribute id in category struct_ref in the
STRUCT_REF category.
struct_ref_seq.seq_align_beg
The sequence position in the entity or biological unit described
in the data block at which the alignment begins.
This data item is a pointer to attribute num in category entity_poly_seq in the
ENTITY_POLY_SEQ category.
struct_ref_seq.seq_align_end
The sequence position in the entity or biological unit described
in the data block at which the alignment ends.
This data item is a pointer to attribute num in category entity_poly_seq in the
ENTITY_POLY_SEQ category.
struct_ref_seq.align_id
The value of attribute align_id in category struct_ref_seq must uniquely identify a
record in the STRUCT_REF_SEQ list.
Note that this item need not be a number; it can be any unique
identifier.
struct_ref_seq_dif
Data items in the STRUCT_REF_SEQ_DIF category provide a
mechanism for indicating and annotating point differences
between the sequence of the entity or biological unit described
in the data block and the sequence of the referenced database
entry.
Example 1 - based on laboratory records for CAP-DNA complex.
<PDBx:struct_ref_seq_difCategory>
<PDBx:struct_ref_seq_dif pdbx_ordinal="1">
<PDBx:align_id>algn2</PDBx:align_id>
<PDBx:db_mon_id>GLU</PDBx:db_mon_id>
<PDBx:details> A point mutation was introduced in the CAP at position 181
substituting PHE for GLU.</PDBx:details>
<PDBx:mon_id>PHE</PDBx:mon_id>
<PDBx:seq_num>181</PDBx:seq_num>
</PDBx:struct_ref_seq_dif>
</PDBx:struct_ref_seq_difCategory>
1
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
struct_ref_seq_difCategory
This property indicates that datablock
has a category element struct_ref_seq_dif.
struct_ref_seq_difItem
Abstract Datatype property for struct_ref_seq_dif items.
reference_to_struct_ref_seq_dif
cross-reference to struct_ref_seq_dif
struct_ref_seq_dif.align_id
This data item is a pointer to attribute align_id in category struct_ref_seq in
the STRUCT_REF_SEQ category.
struct_ref_seq_dif.db_mon_id
The monomer type found at this position in the referenced
database entry.
This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP
category.
struct_ref_seq_dif.details
A description of special aspects of the point differences
between the sequence of the entity or biological unit described
in the data block and that in the referenced database entry.
struct_ref_seq_dif.mon_id
The monomer type found at this position in the sequence of
the entity or biological unit described in this data block.
This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP
category.
struct_ref_seq_dif.pdbx_auth_seq_num
Insertion code in PDB sequence
1
2
struct_ref_seq_dif.pdbx_pdb_id_code
The PDB ID code.
1BBP
struct_ref_seq_dif.pdbx_pdb_ins_code
Insertion code in PDB sequence
1
2
struct_ref_seq_dif.pdbx_pdb_strand_id
PDB strand/chain id.
A
B
struct_ref_seq_dif.pdbx_seq_db_accession_code
Sequence database accession number.
P07617
struct_ref_seq_dif.pdbx_seq_db_name
Sequence database name.
SWS
struct_ref_seq_dif.pdbx_seq_db_seq_num
Sequence database sequence number.
142
struct_ref_seq_dif.seq_num
This data item is a pointer to attribute num in category entity_poly_seq in the
ENTITY_POLY_SEQ category.
struct_ref_seq_dif.pdbx_ordinal
A synthetic integer primary key for this category.
struct_sheet
Data items in the STRUCT_SHEET category record details about
the beta-sheets.
Example 1 - simple beta-barrel.
N O N O N O N O N O N O
10--11--12--13--14--15--16--17--18--19--20 strand_a
N O N O N O N O N O
/ \ / \ / \ / \ / \
N O N O N O N O N O N O
30--31--32--33--34--35--36--37--38--39--40 strand_b
N O N O N O N O N O
/ \ / \ / \ / \ / \
N O N O N O N O N O N O
50--51--52--53--54--55--56--57--58--59--60 strand_c
N O N O N O N O N O
/ \ / \ / \ / \ / \
N O N O N O N O N O N O
70--71--72--73--74--75--76--77--78--79--80 strand_d
N O N O N O N O N O
/ \ / \ / \ / \ / \
N O N O N O N O N O N O
90--91--92--93--94--95--96--97--98--99-100 strand_e
N O N O N O N O N O
/ \ / \ / \ / \ / \
N O N O N O N O N O N O
110-111-112-113-114-115-116-117-118-119-120 strand_f
N O N O N O N O N O
/ \ / \ / \ / \ / \
N O N O N O N O N O N O
130-131-132-133-134-135-136-137-138-139-140 strand_g
N O N O N O N O N O
/ \ / \ / \ / \ / \
N O N O N O N O N O N O
150-151-152-153-154-155-156-157-158-159-160 strand_h
N O N O N O N O N O
/ \ / \ / \ / \ / \
<PDBx:struct_sheetCategory>
<PDBx:struct_sheet id="sheet_1">
<PDBx:details></PDBx:details>
<PDBx:number_strands>8</PDBx:number_strands>
<PDBx:type>beta-barrel</PDBx:type>
</PDBx:struct_sheet>
</PDBx:struct_sheetCategory>
Example 2 - five stranded mixed-sense sheet with one two-piece strand.
N O N O N O N O
-10--11--12--13--14--15--16--17--18-> strand_a
N O N O N O N O N O
| | | | | | | | | |
O N O N O N O N O N
<-119-118-117-116-115-114-113-112-111-110- strand_b
O N O N O N O N O N
\ / \ / \ / \ / \
O N O N O N O N O N O N
<-41--40--39--38--37--36--35--34--33--32--31--30- strand_c
O N O N O N O N O N O N
| | | | | | | | | | | |
N O N O N O N O N O N O
strand_d1 -50--51--52-> -90--91--92--93--95--95--96--97-> strand_d2
N O N O N O N O N O
| | | | | | | | | | | |
O N O N O N O N O N O N
<-80--79--78--77--76--75--74--73--72--71--70- strand_e
O N O N O N O N O N
<PDBx:struct_sheetCategory>
<PDBx:struct_sheet id="sheet_2">
<PDBx:details>strand_d is in two pieces</PDBx:details>
<PDBx:number_strands>5</PDBx:number_strands>
<PDBx:type>five stranded, mixed-sense</PDBx:type>
</PDBx:struct_sheet>
</PDBx:struct_sheetCategory>
0
1
0
1
0
1
1
struct_sheetCategory
This property indicates that datablock
has a category element struct_sheet.
struct_sheetItem
Abstract Datatype property for struct_sheet items.
reference_to_struct_sheet
cross-reference to struct_sheet
struct_sheet.details
A description of special aspects of the beta-sheet.
struct_sheet.number_strands
The number of strands in the sheet. If a given range of residues
bulges out from the strands, it is still counted as one strand.
If a strand is composed of two different regions of polypeptide,
it is still counted as one strand, as long as the proper hydrogen-
bonding connections are made to adjacent strands.
struct_sheet.type
A simple descriptor for the type of the sheet.
jelly-roll
Rossmann fold
beta barrel
struct_sheet.id
The value of attribute id in category struct_sheet must uniquely identify a record in
the STRUCT_SHEET list.
Note that this item need not be a number; it can be any unique
identifier.
struct_sheet_hbond
Data items in the STRUCT_SHEET_HBOND category record details
about the hydrogen bonding between residue ranges in a beta-
sheet. It is necessary to treat hydrogen bonding independently
of the designation of ranges, because the hydrogen bonding may
begin in different places for the interactions of a given strand
with the one preceding it and the one following it in the sheet.
Example 1 - simple beta-barrel.
<PDBx:struct_sheet_hbondCategory>
<PDBx:struct_sheet_hbond range_id_1="strand_a" range_id_2="strand_b" sheet_id="sheet_1">
<PDBx:range_1_beg_label_atom_id>N</PDBx:range_1_beg_label_atom_id>
<PDBx:range_1_beg_label_seq_id>11</PDBx:range_1_beg_label_seq_id>
<PDBx:range_1_end_label_atom_id>O</PDBx:range_1_end_label_atom_id>
<PDBx:range_1_end_label_seq_id>19</PDBx:range_1_end_label_seq_id>
<PDBx:range_2_beg_label_atom_id>O</PDBx:range_2_beg_label_atom_id>
<PDBx:range_2_beg_label_seq_id>30</PDBx:range_2_beg_label_seq_id>
<PDBx:range_2_end_label_atom_id>N</PDBx:range_2_end_label_atom_id>
<PDBx:range_2_end_label_seq_id>40</PDBx:range_2_end_label_seq_id>
</PDBx:struct_sheet_hbond>
<PDBx:struct_sheet_hbond range_id_1="strand_b" range_id_2="strand_c" sheet_id="sheet_1">
<PDBx:range_1_beg_label_atom_id>N</PDBx:range_1_beg_label_atom_id>
<PDBx:range_1_beg_label_seq_id>31</PDBx:range_1_beg_label_seq_id>
<PDBx:range_1_end_label_atom_id>O</PDBx:range_1_end_label_atom_id>
<PDBx:range_1_end_label_seq_id>39</PDBx:range_1_end_label_seq_id>
<PDBx:range_2_beg_label_atom_id>O</PDBx:range_2_beg_label_atom_id>
<PDBx:range_2_beg_label_seq_id>50</PDBx:range_2_beg_label_seq_id>
<PDBx:range_2_end_label_atom_id>N</PDBx:range_2_end_label_atom_id>
<PDBx:range_2_end_label_seq_id>60</PDBx:range_2_end_label_seq_id>
</PDBx:struct_sheet_hbond>
<PDBx:struct_sheet_hbond range_id_1="strand_c" range_id_2="strand_d" sheet_id="sheet_1">
<PDBx:range_1_beg_label_atom_id>N</PDBx:range_1_beg_label_atom_id>
<PDBx:range_1_beg_label_seq_id>51</PDBx:range_1_beg_label_seq_id>
<PDBx:range_1_end_label_atom_id>O</PDBx:range_1_end_label_atom_id>
<PDBx:range_1_end_label_seq_id>59</PDBx:range_1_end_label_seq_id>
<PDBx:range_2_beg_label_atom_id>O</PDBx:range_2_beg_label_atom_id>
<PDBx:range_2_beg_label_seq_id>70</PDBx:range_2_beg_label_seq_id>
<PDBx:range_2_end_label_atom_id>N</PDBx:range_2_end_label_atom_id>
<PDBx:range_2_end_label_seq_id>80</PDBx:range_2_end_label_seq_id>
</PDBx:struct_sheet_hbond>
<PDBx:struct_sheet_hbond range_id_1="strand_d" range_id_2="strand_e" sheet_id="sheet_1">
<PDBx:range_1_beg_label_atom_id>N</PDBx:range_1_beg_label_atom_id>
<PDBx:range_1_beg_label_seq_id>71</PDBx:range_1_beg_label_seq_id>
<PDBx:range_1_end_label_atom_id>O</PDBx:range_1_end_label_atom_id>
<PDBx:range_1_end_label_seq_id>89</PDBx:range_1_end_label_seq_id>
<PDBx:range_2_beg_label_atom_id>O</PDBx:range_2_beg_label_atom_id>
<PDBx:range_2_beg_label_seq_id>90</PDBx:range_2_beg_label_seq_id>
<PDBx:range_2_end_label_atom_id>N</PDBx:range_2_end_label_atom_id>
<PDBx:range_2_end_label_seq_id>100</PDBx:range_2_end_label_seq_id>
</PDBx:struct_sheet_hbond>
<PDBx:struct_sheet_hbond range_id_1="strand_e" range_id_2="strand_f" sheet_id="sheet_1">
<PDBx:range_1_beg_label_atom_id>N</PDBx:range_1_beg_label_atom_id>
<PDBx:range_1_beg_label_seq_id>91</PDBx:range_1_beg_label_seq_id>
<PDBx:range_1_end_label_atom_id>O</PDBx:range_1_end_label_atom_id>
<PDBx:range_1_end_label_seq_id>99</PDBx:range_1_end_label_seq_id>
<PDBx:range_2_beg_label_atom_id>O</PDBx:range_2_beg_label_atom_id>
<PDBx:range_2_beg_label_seq_id>110</PDBx:range_2_beg_label_seq_id>
<PDBx:range_2_end_label_atom_id>N</PDBx:range_2_end_label_atom_id>
<PDBx:range_2_end_label_seq_id>120</PDBx:range_2_end_label_seq_id>
</PDBx:struct_sheet_hbond>
<PDBx:struct_sheet_hbond range_id_1="strand_f" range_id_2="strand_g" sheet_id="sheet_1">
<PDBx:range_1_beg_label_atom_id>N</PDBx:range_1_beg_label_atom_id>
<PDBx:range_1_beg_label_seq_id>111</PDBx:range_1_beg_label_seq_id>
<PDBx:range_1_end_label_atom_id>O</PDBx:range_1_end_label_atom_id>
<PDBx:range_1_end_label_seq_id>119</PDBx:range_1_end_label_seq_id>
<PDBx:range_2_beg_label_atom_id>O</PDBx:range_2_beg_label_atom_id>
<PDBx:range_2_beg_label_seq_id>130</PDBx:range_2_beg_label_seq_id>
<PDBx:range_2_end_label_atom_id>N</PDBx:range_2_end_label_atom_id>
<PDBx:range_2_end_label_seq_id>140</PDBx:range_2_end_label_seq_id>
</PDBx:struct_sheet_hbond>
<PDBx:struct_sheet_hbond range_id_1="strand_g" range_id_2="strand_h" sheet_id="sheet_1">
<PDBx:range_1_beg_label_atom_id>N</PDBx:range_1_beg_label_atom_id>
<PDBx:range_1_beg_label_seq_id>131</PDBx:range_1_beg_label_seq_id>
<PDBx:range_1_end_label_atom_id>O</PDBx:range_1_end_label_atom_id>
<PDBx:range_1_end_label_seq_id>139</PDBx:range_1_end_label_seq_id>
<PDBx:range_2_beg_label_atom_id>O</PDBx:range_2_beg_label_atom_id>
<PDBx:range_2_beg_label_seq_id>150</PDBx:range_2_beg_label_seq_id>
<PDBx:range_2_end_label_atom_id>N</PDBx:range_2_end_label_atom_id>
<PDBx:range_2_end_label_seq_id>160</PDBx:range_2_end_label_seq_id>
</PDBx:struct_sheet_hbond>
<PDBx:struct_sheet_hbond range_id_1="strand_h" range_id_2="strand_a" sheet_id="sheet_1">
<PDBx:range_1_beg_label_atom_id>N</PDBx:range_1_beg_label_atom_id>
<PDBx:range_1_beg_label_seq_id>151</PDBx:range_1_beg_label_seq_id>
<PDBx:range_1_end_label_atom_id>O</PDBx:range_1_end_label_atom_id>
<PDBx:range_1_end_label_seq_id>159</PDBx:range_1_end_label_seq_id>
<PDBx:range_2_beg_label_atom_id>O</PDBx:range_2_beg_label_atom_id>
<PDBx:range_2_beg_label_seq_id>10</PDBx:range_2_beg_label_seq_id>
<PDBx:range_2_end_label_atom_id>N</PDBx:range_2_end_label_atom_id>
<PDBx:range_2_end_label_seq_id>180</PDBx:range_2_end_label_seq_id>
</PDBx:struct_sheet_hbond>
</PDBx:struct_sheet_hbondCategory>
Example 2 - five stranded mixed-sense sheet with one two-piece strand.
<PDBx:struct_sheet_hbondCategory>
<PDBx:struct_sheet_hbond range_id_1="strand_a" range_id_2="strand_b" sheet_id="sheet_2">
<PDBx:range_1_beg_label_atom_id>N</PDBx:range_1_beg_label_atom_id>
<PDBx:range_1_beg_label_seq_id>20</PDBx:range_1_beg_label_seq_id>
<PDBx:range_1_end_label_atom_id>O</PDBx:range_1_end_label_atom_id>
<PDBx:range_1_end_label_seq_id>18</PDBx:range_1_end_label_seq_id>
<PDBx:range_2_beg_label_atom_id>O</PDBx:range_2_beg_label_atom_id>
<PDBx:range_2_beg_label_seq_id>119</PDBx:range_2_beg_label_seq_id>
<PDBx:range_2_end_label_atom_id>N</PDBx:range_2_end_label_atom_id>
<PDBx:range_2_end_label_seq_id>111</PDBx:range_2_end_label_seq_id>
</PDBx:struct_sheet_hbond>
<PDBx:struct_sheet_hbond range_id_1="strand_b" range_id_2="strand_c" sheet_id="sheet_2">
<PDBx:range_1_beg_label_atom_id>N</PDBx:range_1_beg_label_atom_id>
<PDBx:range_1_beg_label_seq_id>110</PDBx:range_1_beg_label_seq_id>
<PDBx:range_1_end_label_atom_id>N</PDBx:range_1_end_label_atom_id>
<PDBx:range_1_end_label_seq_id>118</PDBx:range_1_end_label_seq_id>
<PDBx:range_2_beg_label_atom_id>O</PDBx:range_2_beg_label_atom_id>
<PDBx:range_2_beg_label_seq_id>33</PDBx:range_2_beg_label_seq_id>
<PDBx:range_2_end_label_atom_id>O</PDBx:range_2_end_label_atom_id>
<PDBx:range_2_end_label_seq_id>41</PDBx:range_2_end_label_seq_id>
</PDBx:struct_sheet_hbond>
<PDBx:struct_sheet_hbond range_id_1="strand_c" range_id_2="strand_d1" sheet_id="sheet_2">
<PDBx:range_1_beg_label_atom_id>N</PDBx:range_1_beg_label_atom_id>
<PDBx:range_1_beg_label_seq_id>38</PDBx:range_1_beg_label_seq_id>
<PDBx:range_1_end_label_atom_id>O</PDBx:range_1_end_label_atom_id>
<PDBx:range_1_end_label_seq_id>40</PDBx:range_1_end_label_seq_id>
<PDBx:range_2_beg_label_atom_id>O</PDBx:range_2_beg_label_atom_id>
<PDBx:range_2_beg_label_seq_id>52</PDBx:range_2_beg_label_seq_id>
<PDBx:range_2_end_label_atom_id>N</PDBx:range_2_end_label_atom_id>
<PDBx:range_2_end_label_seq_id>50</PDBx:range_2_end_label_seq_id>
</PDBx:struct_sheet_hbond>
<PDBx:struct_sheet_hbond range_id_1="strand_c" range_id_2="strand_d2" sheet_id="sheet_2">
<PDBx:range_1_beg_label_atom_id>N</PDBx:range_1_beg_label_atom_id>
<PDBx:range_1_beg_label_seq_id>30</PDBx:range_1_beg_label_seq_id>
<PDBx:range_1_end_label_atom_id>O</PDBx:range_1_end_label_atom_id>
<PDBx:range_1_end_label_seq_id>36</PDBx:range_1_end_label_seq_id>
<PDBx:range_2_beg_label_atom_id>O</PDBx:range_2_beg_label_atom_id>
<PDBx:range_2_beg_label_seq_id>96</PDBx:range_2_beg_label_seq_id>
<PDBx:range_2_end_label_atom_id>N</PDBx:range_2_end_label_atom_id>
<PDBx:range_2_end_label_seq_id>90</PDBx:range_2_end_label_seq_id>
</PDBx:struct_sheet_hbond>
<PDBx:struct_sheet_hbond range_id_1="strand_d1" range_id_2="strand_e" sheet_id="sheet_2">
<PDBx:range_1_beg_label_atom_id>N</PDBx:range_1_beg_label_atom_id>
<PDBx:range_1_beg_label_seq_id>51</PDBx:range_1_beg_label_seq_id>
<PDBx:range_1_end_label_atom_id>O</PDBx:range_1_end_label_atom_id>
<PDBx:range_1_end_label_seq_id>51</PDBx:range_1_end_label_seq_id>
<PDBx:range_2_beg_label_atom_id>O</PDBx:range_2_beg_label_atom_id>
<PDBx:range_2_beg_label_seq_id>80</PDBx:range_2_beg_label_seq_id>
<PDBx:range_2_end_label_atom_id>N</PDBx:range_2_end_label_atom_id>
<PDBx:range_2_end_label_seq_id>80</PDBx:range_2_end_label_seq_id>
</PDBx:struct_sheet_hbond>
<PDBx:struct_sheet_hbond range_id_1="strand_d2" range_id_2="strand_e" sheet_id="sheet_2">
<PDBx:range_1_beg_label_atom_id>N</PDBx:range_1_beg_label_atom_id>
<PDBx:range_1_beg_label_seq_id>91</PDBx:range_1_beg_label_seq_id>
<PDBx:range_1_end_label_atom_id>O</PDBx:range_1_end_label_atom_id>
<PDBx:range_1_end_label_seq_id>97</PDBx:range_1_end_label_seq_id>
<PDBx:range_2_beg_label_atom_id>O</PDBx:range_2_beg_label_atom_id>
<PDBx:range_2_beg_label_seq_id>76</PDBx:range_2_beg_label_seq_id>
<PDBx:range_2_end_label_atom_id>N</PDBx:range_2_end_label_atom_id>
<PDBx:range_2_end_label_seq_id>70</PDBx:range_2_end_label_seq_id>
</PDBx:struct_sheet_hbond>
</PDBx:struct_sheet_hbondCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
0
1
0
1
1
1
1
1
0
1
0
1
1
1
1
1
0
1
0
1
1
1
1
1
1
1
1
struct_sheet_hbondCategory
This property indicates that datablock
has a category element struct_sheet_hbond.
struct_sheet_hbondItem
Abstract Datatype property for struct_sheet_hbond items.
reference_to_struct_sheet_hbond
cross-reference to struct_sheet_hbond
struct_sheet_hbond.pdbx_range_1_beg_PDB_ins_code
Pointer to attribute pdbx_PDB_ins_code in category atom_site.
struct_sheet_hbond.pdbx_range_1_beg_auth_asym_id
Pointer to attribute auth_asym_id in category atom_site.
struct_sheet_hbond.pdbx_range_1_beg_auth_comp_id
Pointer to attribute auth_comp_id in category atom_site
struct_sheet_hbond.pdbx_range_1_beg_label_asym_id
Pointer to attribute label_asym_id in category atom_site.
struct_sheet_hbond.pdbx_range_1_beg_label_comp_id
Pointer to attribute label_comp_id in category atom_site
struct_sheet_hbond.pdbx_range_1_end_PDB_ins_code
Pointer to attribute pdbx_PDB_ins_code in category atom_site.
struct_sheet_hbond.pdbx_range_1_end_auth_asym_id
Pointer to attribute auth_comp_id in category atom_site.
struct_sheet_hbond.pdbx_range_1_end_auth_comp_id
Pointer to attribute auth_comp_id in category atom_site.
struct_sheet_hbond.pdbx_range_1_end_label_asym_id
Pointer to attribute label_asym_id in category atom_site.
struct_sheet_hbond.pdbx_range_1_end_label_comp_id
Pointer to attribute label_comp_id in category atom_site.
struct_sheet_hbond.pdbx_range_2_beg_PDB_ins_code
Pointer to attribute pdbx_PDB_ins_code in category atom_site.
struct_sheet_hbond.pdbx_range_2_beg_label_asym_id
Pointer to attribute label_asym_id in category atom_site.
struct_sheet_hbond.pdbx_range_2_beg_label_comp_id
Pointer to attribute label_comp_id in category atom_site.
struct_sheet_hbond.pdbx_range_2_end_label_asym_id
Pointer to attribute label_asym_id in category atom_site.
struct_sheet_hbond.pdbx_range_2_end_label_comp_id
Pointer to attribute label_comp_id in category atom_site.
struct_sheet_hbond.pdbx_range_2_end_label_ins_code
Place holder for PDB insertion code.
struct_sheet_hbond.range_1_beg_auth_atom_id
A component of the identifier for the residue for the first
partner of the first hydrogen bond between two residue ranges
in a sheet.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
struct_sheet_hbond.range_1_beg_auth_seq_id
A component of the identifier for the residue for the first
partner of the first hydrogen bond between two residue ranges
in a sheet.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
struct_sheet_hbond.range_1_beg_label_atom_id
A component of the identifier for the residue for the first
partner of the first hydrogen bond between two residue ranges
in a sheet.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
struct_sheet_hbond.range_1_beg_label_seq_id
A component of the identifier for the residue for the first
partner of the first hydrogen bond between two residue ranges
in a sheet.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
struct_sheet_hbond.range_1_end_auth_atom_id
A component of the identifier for the residue for the first
partner of the last hydrogen bond between two residue ranges in
a sheet.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
struct_sheet_hbond.range_1_end_auth_seq_id
A component of the identifier for the residue for the first
partner of the last hydrogen bond between two residue ranges in
a sheet.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
struct_sheet_hbond.range_1_end_label_atom_id
A component of the identifier for the residue for the first
partner of the last hydrogen bond between two residue ranges in
a sheet.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
struct_sheet_hbond.range_1_end_label_seq_id
A component of the identifier for the residue for the first
partner of the last hydrogen bond between two residue ranges in
a sheet.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
struct_sheet_hbond.range_2_beg_auth_atom_id
A component of the identifier for the residue for the second
partner of the first hydrogen bond between two residue ranges
in a sheet.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
struct_sheet_hbond.range_2_beg_auth_seq_id
A component of the identifier for the residue for the second
partner of the first hydrogen bond between two residue ranges
in a sheet.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
struct_sheet_hbond.range_2_beg_label_atom_id
A component of the identifier for the residue for the second
partner of the first hydrogen bond between two residue ranges
in a sheet.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
struct_sheet_hbond.range_2_beg_label_seq_id
A component of the identifier for the residue for the second
partner of the first hydrogen bond between two residue ranges
in a sheet.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
struct_sheet_hbond.range_2_end_auth_atom_id
A component of the identifier for the residue for the second
partner of the last hydrogen bond between two residue ranges in
a sheet.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
struct_sheet_hbond.range_2_end_auth_seq_id
A component of the identifier for the residue for the second
partner of the last hydrogen bond between two residue ranges in
a sheet.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
struct_sheet_hbond.range_2_end_label_atom_id
A component of the identifier for the residue for the second
partner of the last hydrogen bond between two residue ranges in
a sheet.
This data item is a pointer to attribute label_atom_id in category atom_site in the
ATOM_SITE category.
struct_sheet_hbond.range_2_end_label_seq_id
A component of the identifier for the residue for the second
partner of the last hydrogen bond between two residue ranges in
a sheet.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
struct_sheet_hbond.range_id_1
This data item is a pointer to attribute id in category struct_sheet_range in
the STRUCT_SHEET_RANGE category.
struct_sheet_hbond.range_id_2
This data item is a pointer to attribute id in category struct_sheet_range in
the STRUCT_SHEET_RANGE category.
struct_sheet_hbond.sheet_id
This data item is a pointer to attribute id in category struct_sheet in the
STRUCT_SHEET category.
struct_sheet_order
Data items in the STRUCT_SHEET_ORDER category record details
about the order of the residue ranges that form a beta-sheet.
All order links are pairwise and the specified pairs are
assumed to be adjacent to one another in the sheet. These data
items are an alternative to the STRUCT_SHEET_TOPOLOGY data
items and they allow all manner of sheets to be described.
Example 1 - simple beta-barrel.
<PDBx:struct_sheet_orderCategory>
<PDBx:struct_sheet_order range_id_1="strand_a" range_id_2="strand_b" sheet_id="sheet_1">
<PDBx:offset>+1</PDBx:offset>
<PDBx:sense>parallel</PDBx:sense>
</PDBx:struct_sheet_order>
<PDBx:struct_sheet_order range_id_1="strand_b" range_id_2="strand_c" sheet_id="sheet_1">
<PDBx:offset>+1</PDBx:offset>
<PDBx:sense>parallel</PDBx:sense>
</PDBx:struct_sheet_order>
<PDBx:struct_sheet_order range_id_1="strand_c" range_id_2="strand_d" sheet_id="sheet_1">
<PDBx:offset>+1</PDBx:offset>
<PDBx:sense>parallel</PDBx:sense>
</PDBx:struct_sheet_order>
<PDBx:struct_sheet_order range_id_1="strand_d" range_id_2="strand_e" sheet_id="sheet_1">
<PDBx:offset>+1</PDBx:offset>
<PDBx:sense>parallel</PDBx:sense>
</PDBx:struct_sheet_order>
<PDBx:struct_sheet_order range_id_1="strand_e" range_id_2="strand_f" sheet_id="sheet_1">
<PDBx:offset>+1</PDBx:offset>
<PDBx:sense>parallel</PDBx:sense>
</PDBx:struct_sheet_order>
<PDBx:struct_sheet_order range_id_1="strand_f" range_id_2="strand_g" sheet_id="sheet_1">
<PDBx:offset>+1</PDBx:offset>
<PDBx:sense>parallel</PDBx:sense>
</PDBx:struct_sheet_order>
<PDBx:struct_sheet_order range_id_1="strand_g" range_id_2="strand_h" sheet_id="sheet_1">
<PDBx:offset>+1</PDBx:offset>
<PDBx:sense>parallel</PDBx:sense>
</PDBx:struct_sheet_order>
<PDBx:struct_sheet_order range_id_1="strand_h" range_id_2="strand_a" sheet_id="sheet_1">
<PDBx:offset>+1</PDBx:offset>
<PDBx:sense>parallel</PDBx:sense>
</PDBx:struct_sheet_order>
</PDBx:struct_sheet_orderCategory>
Example 2 - five stranded mixed-sense sheet with one two-piece strand.
<PDBx:struct_sheet_orderCategory>
<PDBx:struct_sheet_order range_id_1="strand_a" range_id_2="strand_b" sheet_id="sheet_2">
<PDBx:offset>+1</PDBx:offset>
<PDBx:sense>anti-parallel</PDBx:sense>
</PDBx:struct_sheet_order>
<PDBx:struct_sheet_order range_id_1="strand_b" range_id_2="strand_c" sheet_id="sheet_2">
<PDBx:offset>+1</PDBx:offset>
<PDBx:sense>parallel</PDBx:sense>
</PDBx:struct_sheet_order>
<PDBx:struct_sheet_order range_id_1="strand_c" range_id_2="strand_d1" sheet_id="sheet_2">
<PDBx:offset>+1</PDBx:offset>
<PDBx:sense>anti-parallel</PDBx:sense>
</PDBx:struct_sheet_order>
<PDBx:struct_sheet_order range_id_1="strand_c" range_id_2="strand_d2" sheet_id="sheet_2">
<PDBx:offset>+1</PDBx:offset>
<PDBx:sense>anti-parallel</PDBx:sense>
</PDBx:struct_sheet_order>
<PDBx:struct_sheet_order range_id_1="strand_d1" range_id_2="strand_e" sheet_id="sheet_2">
<PDBx:offset>+1</PDBx:offset>
<PDBx:sense>anti-parallel</PDBx:sense>
</PDBx:struct_sheet_order>
<PDBx:struct_sheet_order range_id_1="strand_d2" range_id_2="strand_e" sheet_id="sheet_2">
<PDBx:offset>+1</PDBx:offset>
<PDBx:sense>anti-parallel</PDBx:sense>
</PDBx:struct_sheet_order>
</PDBx:struct_sheet_orderCategory>
0
1
0
1
1
1
1
struct_sheet_orderCategory
This property indicates that datablock
has a category element struct_sheet_order.
struct_sheet_orderItem
Abstract Datatype property for struct_sheet_order items.
reference_to_struct_sheet_order
cross-reference to struct_sheet_order
struct_sheet_order.offset
Designates the relative position in the sheet, plus or minus, of
the second residue range to the first.
parallel
anti-parallel
A flag to indicate whether the two designated residue ranges are
parallel or antiparallel to one another.
struct_sheet_order.range_id_1
This data item is a pointer to attribute id in category struct_sheet_range in
the STRUCT_SHEET_RANGE category.
struct_sheet_order.range_id_2
This data item is a pointer to attribute id in category struct_sheet_range in
the STRUCT_SHEET_RANGE category.
struct_sheet_order.sheet_id
This data item is a pointer to attribute id in category struct_sheet in the
STRUCT_SHEET category.
struct_sheet_range
Data items in the STRUCT_SHEET_RANGE category record details
about the residue ranges that form a beta-sheet. Residues are
included in a range if they made beta-sheet-type hydrogen-bonding
interactions with at least one adjacent strand and if there are
at least two residues in the range.
Example 1 - simple beta-barrel.
<PDBx:struct_sheet_rangeCategory>
<PDBx:struct_sheet_range id="strand_a" sheet_id="sheet_1">
<PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id>
<PDBx:beg_label_comp_id>ala</PDBx:beg_label_comp_id>
<PDBx:beg_label_seq_id>20</PDBx:beg_label_seq_id>
<PDBx:end_label_asym_id>A</PDBx:end_label_asym_id>
<PDBx:end_label_comp_id>ala</PDBx:end_label_comp_id>
<PDBx:end_label_seq_id>30</PDBx:end_label_seq_id>
<PDBx:symmetry>1_555</PDBx:symmetry>
</PDBx:struct_sheet_range>
<PDBx:struct_sheet_range id="strand_b" sheet_id="sheet_1">
<PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id>
<PDBx:beg_label_comp_id>ala</PDBx:beg_label_comp_id>
<PDBx:beg_label_seq_id>40</PDBx:beg_label_seq_id>
<PDBx:end_label_asym_id>A</PDBx:end_label_asym_id>
<PDBx:end_label_comp_id>ala</PDBx:end_label_comp_id>
<PDBx:end_label_seq_id>50</PDBx:end_label_seq_id>
<PDBx:symmetry>1_555</PDBx:symmetry>
</PDBx:struct_sheet_range>
<PDBx:struct_sheet_range id="strand_c" sheet_id="sheet_1">
<PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id>
<PDBx:beg_label_comp_id>ala</PDBx:beg_label_comp_id>
<PDBx:beg_label_seq_id>60</PDBx:beg_label_seq_id>
<PDBx:end_label_asym_id>A</PDBx:end_label_asym_id>
<PDBx:end_label_comp_id>ala</PDBx:end_label_comp_id>
<PDBx:end_label_seq_id>70</PDBx:end_label_seq_id>
<PDBx:symmetry>1_555</PDBx:symmetry>
</PDBx:struct_sheet_range>
<PDBx:struct_sheet_range id="strand_d" sheet_id="sheet_1">
<PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id>
<PDBx:beg_label_comp_id>ala</PDBx:beg_label_comp_id>
<PDBx:beg_label_seq_id>80</PDBx:beg_label_seq_id>
<PDBx:end_label_asym_id>A</PDBx:end_label_asym_id>
<PDBx:end_label_comp_id>ala</PDBx:end_label_comp_id>
<PDBx:end_label_seq_id>90</PDBx:end_label_seq_id>
<PDBx:symmetry>1_555</PDBx:symmetry>
</PDBx:struct_sheet_range>
<PDBx:struct_sheet_range id="strand_e" sheet_id="sheet_1">
<PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id>
<PDBx:beg_label_comp_id>ala</PDBx:beg_label_comp_id>
<PDBx:beg_label_seq_id>100</PDBx:beg_label_seq_id>
<PDBx:end_label_asym_id>A</PDBx:end_label_asym_id>
<PDBx:end_label_comp_id>ala</PDBx:end_label_comp_id>
<PDBx:end_label_seq_id>110</PDBx:end_label_seq_id>
<PDBx:symmetry>1_555</PDBx:symmetry>
</PDBx:struct_sheet_range>
<PDBx:struct_sheet_range id="strand_f" sheet_id="sheet_1">
<PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id>
<PDBx:beg_label_comp_id>ala</PDBx:beg_label_comp_id>
<PDBx:beg_label_seq_id>120</PDBx:beg_label_seq_id>
<PDBx:end_label_asym_id>A</PDBx:end_label_asym_id>
<PDBx:end_label_comp_id>ala</PDBx:end_label_comp_id>
<PDBx:end_label_seq_id>130</PDBx:end_label_seq_id>
<PDBx:symmetry>1_555</PDBx:symmetry>
</PDBx:struct_sheet_range>
<PDBx:struct_sheet_range id="strand_g" sheet_id="sheet_1">
<PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id>
<PDBx:beg_label_comp_id>ala</PDBx:beg_label_comp_id>
<PDBx:beg_label_seq_id>140</PDBx:beg_label_seq_id>
<PDBx:end_label_asym_id>A</PDBx:end_label_asym_id>
<PDBx:end_label_comp_id>ala</PDBx:end_label_comp_id>
<PDBx:end_label_seq_id>150</PDBx:end_label_seq_id>
<PDBx:symmetry>1_555</PDBx:symmetry>
</PDBx:struct_sheet_range>
<PDBx:struct_sheet_range id="strand_h" sheet_id="sheet_1">
<PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id>
<PDBx:beg_label_comp_id>ala</PDBx:beg_label_comp_id>
<PDBx:beg_label_seq_id>160</PDBx:beg_label_seq_id>
<PDBx:end_label_asym_id>A</PDBx:end_label_asym_id>
<PDBx:end_label_comp_id>ala</PDBx:end_label_comp_id>
<PDBx:end_label_seq_id>170</PDBx:end_label_seq_id>
<PDBx:symmetry>1_555</PDBx:symmetry>
</PDBx:struct_sheet_range>
</PDBx:struct_sheet_rangeCategory>
Example 2 - five stranded mixed-sense sheet with one two-piece strand.
<PDBx:struct_sheet_rangeCategory>
<PDBx:struct_sheet_range id="strand_a" sheet_id="sheet_2">
<PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id>
<PDBx:beg_label_comp_id>ala</PDBx:beg_label_comp_id>
<PDBx:beg_label_seq_id>10</PDBx:beg_label_seq_id>
<PDBx:end_label_asym_id>A</PDBx:end_label_asym_id>
<PDBx:end_label_comp_id>ala</PDBx:end_label_comp_id>
<PDBx:end_label_seq_id>18</PDBx:end_label_seq_id>
<PDBx:symmetry>1_555</PDBx:symmetry>
</PDBx:struct_sheet_range>
<PDBx:struct_sheet_range id="strand_b" sheet_id="sheet_2">
<PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id>
<PDBx:beg_label_comp_id>ala</PDBx:beg_label_comp_id>
<PDBx:beg_label_seq_id>110</PDBx:beg_label_seq_id>
<PDBx:end_label_asym_id>A</PDBx:end_label_asym_id>
<PDBx:end_label_comp_id>ala</PDBx:end_label_comp_id>
<PDBx:end_label_seq_id>119</PDBx:end_label_seq_id>
<PDBx:symmetry>1_555</PDBx:symmetry>
</PDBx:struct_sheet_range>
<PDBx:struct_sheet_range id="strand_c" sheet_id="sheet_2">
<PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id>
<PDBx:beg_label_comp_id>ala</PDBx:beg_label_comp_id>
<PDBx:beg_label_seq_id>30</PDBx:beg_label_seq_id>
<PDBx:end_label_asym_id>A</PDBx:end_label_asym_id>
<PDBx:end_label_comp_id>ala</PDBx:end_label_comp_id>
<PDBx:end_label_seq_id>41</PDBx:end_label_seq_id>
<PDBx:symmetry>1_555</PDBx:symmetry>
</PDBx:struct_sheet_range>
<PDBx:struct_sheet_range id="strand_d1" sheet_id="sheet_2">
<PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id>
<PDBx:beg_label_comp_id>ala</PDBx:beg_label_comp_id>
<PDBx:beg_label_seq_id>50</PDBx:beg_label_seq_id>
<PDBx:end_label_asym_id>A</PDBx:end_label_asym_id>
<PDBx:end_label_comp_id>ala</PDBx:end_label_comp_id>
<PDBx:end_label_seq_id>52</PDBx:end_label_seq_id>
<PDBx:symmetry>1_555</PDBx:symmetry>
</PDBx:struct_sheet_range>
<PDBx:struct_sheet_range id="strand_d2" sheet_id="sheet_2">
<PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id>
<PDBx:beg_label_comp_id>ala</PDBx:beg_label_comp_id>
<PDBx:beg_label_seq_id>90</PDBx:beg_label_seq_id>
<PDBx:end_label_asym_id>A</PDBx:end_label_asym_id>
<PDBx:end_label_comp_id>ala</PDBx:end_label_comp_id>
<PDBx:end_label_seq_id>97</PDBx:end_label_seq_id>
<PDBx:symmetry>1_555</PDBx:symmetry>
</PDBx:struct_sheet_range>
<PDBx:struct_sheet_range id="strand_e" sheet_id="sheet_2">
<PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id>
<PDBx:beg_label_comp_id>ala</PDBx:beg_label_comp_id>
<PDBx:beg_label_seq_id>70</PDBx:beg_label_seq_id>
<PDBx:end_label_asym_id>A</PDBx:end_label_asym_id>
<PDBx:end_label_comp_id>ala</PDBx:end_label_comp_id>
<PDBx:end_label_seq_id>80</PDBx:end_label_seq_id>
<PDBx:symmetry>1_555</PDBx:symmetry>
</PDBx:struct_sheet_range>
</PDBx:struct_sheet_rangeCategory>
0
1
0
1
0
1
1
1
1
1
1
1
0
1
0
1
0
1
1
1
1
1
1
1
0
1
0
1
0
1
1
1
struct_sheet_rangeCategory
This property indicates that datablock
has a category element struct_sheet_range.
struct_sheet_rangeItem
Abstract Datatype property for struct_sheet_range items.
reference_to_struct_sheet_range
cross-reference to struct_sheet_range
struct_sheet_range.beg_auth_asym_id
A component of the identifier for the residue at which the
beta-sheet range begins.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
struct_sheet_range.beg_auth_comp_id
A component of the identifier for the residue at which the
beta-sheet range begins.
This data item is a pointer to attribute auth_comp_id in category atom_site in
the ATOM_SITE category.
struct_sheet_range.beg_auth_seq_id
A component of the identifier for the residue at which the
beta-sheet range begins.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
struct_sheet_range.beg_label_asym_id
A component of the identifier for the residue at which the
beta-sheet range begins.
This data item is a pointer to attribute id in category struct_asym in the
STRUCT_ASYM category.
struct_sheet_range.beg_label_comp_id
A component of the identifier for the residue at which the
beta-sheet range begins.
This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP
category.
struct_sheet_range.beg_label_seq_id
A component of the identifier for the residue at which the
beta-sheet range begins.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
struct_sheet_range.end_auth_asym_id
A component of the identifier for the residue at which the
beta-sheet range ends.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
struct_sheet_range.end_auth_comp_id
A component of the identifier for the residue at which the
beta-sheet range ends.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
struct_sheet_range.end_auth_seq_id
A component of the identifier for the residue at which the
beta-sheet range ends.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
struct_sheet_range.end_label_asym_id
A component of the identifier for the residue at which the
beta-sheet range ends.
This data item is a pointer to attribute id in category struct_asym in the
STRUCT_ASYM category.
struct_sheet_range.end_label_comp_id
A component of the identifier for the residue at which the
beta-sheet range ends.
This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP
category.
struct_sheet_range.end_label_seq_id
A component of the identifier for the residue at which the
beta-sheet range ends.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
struct_sheet_range.pdbx_beg_PDB_ins_code
A component of the identifier for the residue at which the
beta sheet range begins. Insertion code.
struct_sheet_range.pdbx_end_PDB_ins_code
A component of the identifier for the residue at which the
beta sheet range ends. Insertion code.
struct_sheet_range.symmetry
Describes the symmetry operation that should be applied to the
residues delimited by the start and end designators in
order to generate the appropriate strand in this sheet.
struct_sheet_range.id
The value of attribute id in category struct_sheet_range must uniquely identify a
range in a given sheet in the STRUCT_SHEET_RANGE list.
Note that this item need not be a number; it can be any unique
identifier.
struct_sheet_range.sheet_id
This data item is a pointer to attribute id in category struct_sheet in the
STRUCT_SHEET category.
struct_sheet_topology
Data items in the STRUCT_SHEET_TOPOLOGY category record details
about the topology of the residue ranges that form a beta-sheet.
All topology links are pairwise and the specified pairs are
assumed to be successive in the amino-acid sequence. These
data items are useful in describing various simple and complex
folds, but they become inadequate when the strands in the sheet
come from more than one chain. The
STRUCT_SHEET_ORDER data items can be used to describe
single- and multiple-chain-containing sheets.
Example 1 - simple beta-barrel.
<PDBx:struct_sheet_topologyCategory>
<PDBx:struct_sheet_topology range_id_1="strand_a" range_id_2="strand_b" sheet_id="sheet_1">
<PDBx:offset>+1</PDBx:offset>
<PDBx:sense>parallel</PDBx:sense>
</PDBx:struct_sheet_topology>
<PDBx:struct_sheet_topology range_id_1="strand_b" range_id_2="strand_c" sheet_id="sheet_1">
<PDBx:offset>+1</PDBx:offset>
<PDBx:sense>parallel</PDBx:sense>
</PDBx:struct_sheet_topology>
<PDBx:struct_sheet_topology range_id_1="strand_c" range_id_2="strand_d" sheet_id="sheet_1">
<PDBx:offset>+1</PDBx:offset>
<PDBx:sense>parallel</PDBx:sense>
</PDBx:struct_sheet_topology>
<PDBx:struct_sheet_topology range_id_1="strand_d" range_id_2="strand_e" sheet_id="sheet_1">
<PDBx:offset>+1</PDBx:offset>
<PDBx:sense>parallel</PDBx:sense>
</PDBx:struct_sheet_topology>
<PDBx:struct_sheet_topology range_id_1="strand_e" range_id_2="strand_f" sheet_id="sheet_1">
<PDBx:offset>+1</PDBx:offset>
<PDBx:sense>parallel</PDBx:sense>
</PDBx:struct_sheet_topology>
<PDBx:struct_sheet_topology range_id_1="strand_f" range_id_2="strand_g" sheet_id="sheet_1">
<PDBx:offset>+1</PDBx:offset>
<PDBx:sense>parallel</PDBx:sense>
</PDBx:struct_sheet_topology>
<PDBx:struct_sheet_topology range_id_1="strand_g" range_id_2="strand_h" sheet_id="sheet_1">
<PDBx:offset>+1</PDBx:offset>
<PDBx:sense>parallel</PDBx:sense>
</PDBx:struct_sheet_topology>
<PDBx:struct_sheet_topology range_id_1="strand_h" range_id_2="strand_a" sheet_id="sheet_1">
<PDBx:offset>+1</PDBx:offset>
<PDBx:sense>parallel</PDBx:sense>
</PDBx:struct_sheet_topology>
</PDBx:struct_sheet_topologyCategory>
Example 2 - five stranded mixed-sense sheet with one two-piece strand.
<PDBx:struct_sheet_topologyCategory>
<PDBx:struct_sheet_topology range_id_1="strand_a" range_id_2="strand_c" sheet_id="sheet_2">
<PDBx:offset>+2</PDBx:offset>
<PDBx:sense>anti-parallel</PDBx:sense>
</PDBx:struct_sheet_topology>
<PDBx:struct_sheet_topology range_id_1="strand_c" range_id_2="strand_d1" sheet_id="sheet_2">
<PDBx:offset>+1</PDBx:offset>
<PDBx:sense>anti-parallel</PDBx:sense>
</PDBx:struct_sheet_topology>
<PDBx:struct_sheet_topology range_id_1="strand_d1" range_id_2="strand_e" sheet_id="sheet_2">
<PDBx:offset>+1</PDBx:offset>
<PDBx:sense>anti-parallel</PDBx:sense>
</PDBx:struct_sheet_topology>
<PDBx:struct_sheet_topology range_id_1="strand_e" range_id_2="strand_d2" sheet_id="sheet_2">
<PDBx:offset>-1</PDBx:offset>
<PDBx:sense>anti-parallel</PDBx:sense>
</PDBx:struct_sheet_topology>
<PDBx:struct_sheet_topology range_id_1="strand_d2" range_id_2="strand_b" sheet_id="sheet_2">
<PDBx:offset>-2</PDBx:offset>
<PDBx:sense>anti-parallel</PDBx:sense>
</PDBx:struct_sheet_topology>
</PDBx:struct_sheet_topologyCategory>
0
1
0
1
1
1
1
struct_sheet_topologyCategory
This property indicates that datablock
has a category element struct_sheet_topology.
struct_sheet_topologyItem
Abstract Datatype property for struct_sheet_topology items.
reference_to_struct_sheet_topology
cross-reference to struct_sheet_topology
struct_sheet_topology.offset
Designates the relative position in the sheet, plus or minus, of
the second residue range to the first.
parallel
anti-parallel
A flag to indicate whether the two designated residue ranges are
parallel or antiparallel to one another.
struct_sheet_topology.range_id_1
This data item is a pointer to attribute id in category struct_sheet_range in
the STRUCT_SHEET_RANGE category.
struct_sheet_topology.range_id_2
This data item is a pointer to attribute id in category struct_sheet_range in
the STRUCT_SHEET_RANGE category.
struct_sheet_topology.sheet_id
This data item is a pointer to attribute id in category struct_sheet in the
STRUCT_SHEET category.
struct_site
Data items in the STRUCT_SITE category record details about
portions of the structure that contribute to structurally
relevant sites (e.g. active sites, substrate-binding subsites,
metal-coordination sites).
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:struct_siteCategory>
<PDBx:struct_site id="P2 site C">
<PDBx:details> residues with a contact < 3.7 \%A to an atom in the P2
moiety of the inhibitor in the conformation with
_struct_asym.id = C</PDBx:details>
</PDBx:struct_site>
<PDBx:struct_site id="P2 site D">
<PDBx:details> residues with a contact < 3.7 \%A to an atom in the P1
moiety of the inhibitor in the conformation with
_struct_asym.id = D)</PDBx:details>
</PDBx:struct_site>
</PDBx:struct_siteCategory>
0
1
0
1
0
1
1
struct_siteCategory
This property indicates that datablock
has a category element struct_site.
struct_siteItem
Abstract Datatype property for struct_site items.
reference_to_struct_site
cross-reference to struct_site
struct_site.details
A description of special aspects of the site.
struct_site.pdbx_evidence_code
Source of evidence supporting the assignment of this site.
SOFTWARE
AUTHOR
UNKNOWN
struct_site.pdbx_num_residues
Number of residues in the site.
struct_site.id
The value of attribute id in category struct_site must uniquely identify a record in
the STRUCT_SITE list.
Note that this item need not be a number; it can be any unique
identifier.
struct_site_gen
Data items in the STRUCT_SITE_GEN category record details about
the generation of portions of the structure that contribute to
structurally relevant sites.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:struct_site_genCategory>
<PDBx:struct_site_gen id="1" site_id="1">
<PDBx:details></PDBx:details>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_comp_id>VAL</PDBx:label_comp_id>
<PDBx:label_seq_id>32</PDBx:label_seq_id>
<PDBx:symmetry>1_555</PDBx:symmetry>
</PDBx:struct_site_gen>
<PDBx:struct_site_gen id="2" site_id="1">
<PDBx:details></PDBx:details>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_comp_id>ILE</PDBx:label_comp_id>
<PDBx:label_seq_id>47</PDBx:label_seq_id>
<PDBx:symmetry>1_555</PDBx:symmetry>
</PDBx:struct_site_gen>
<PDBx:struct_site_gen id="3" site_id="1">
<PDBx:details></PDBx:details>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_comp_id>VAL</PDBx:label_comp_id>
<PDBx:label_seq_id>82</PDBx:label_seq_id>
<PDBx:symmetry>1_555</PDBx:symmetry>
</PDBx:struct_site_gen>
<PDBx:struct_site_gen id="4" site_id="1">
<PDBx:details></PDBx:details>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_comp_id>ILE</PDBx:label_comp_id>
<PDBx:label_seq_id>84</PDBx:label_seq_id>
<PDBx:symmetry>1_555</PDBx:symmetry>
</PDBx:struct_site_gen>
<PDBx:struct_site_gen id="5" site_id="2">
<PDBx:details></PDBx:details>
<PDBx:label_asym_id>B</PDBx:label_asym_id>
<PDBx:label_comp_id>VAL</PDBx:label_comp_id>
<PDBx:label_seq_id>232</PDBx:label_seq_id>
<PDBx:symmetry>1_555</PDBx:symmetry>
</PDBx:struct_site_gen>
<PDBx:struct_site_gen id="6" site_id="2">
<PDBx:details></PDBx:details>
<PDBx:label_asym_id>B</PDBx:label_asym_id>
<PDBx:label_comp_id>ILE</PDBx:label_comp_id>
<PDBx:label_seq_id>247</PDBx:label_seq_id>
<PDBx:symmetry>1_555</PDBx:symmetry>
</PDBx:struct_site_gen>
<PDBx:struct_site_gen id="7" site_id="2">
<PDBx:details></PDBx:details>
<PDBx:label_asym_id>B</PDBx:label_asym_id>
<PDBx:label_comp_id>VAL</PDBx:label_comp_id>
<PDBx:label_seq_id>282</PDBx:label_seq_id>
<PDBx:symmetry>1_555</PDBx:symmetry>
</PDBx:struct_site_gen>
<PDBx:struct_site_gen id="8" site_id="2">
<PDBx:details></PDBx:details>
<PDBx:label_asym_id>B</PDBx:label_asym_id>
<PDBx:label_comp_id>ILE</PDBx:label_comp_id>
<PDBx:label_seq_id>284</PDBx:label_seq_id>
<PDBx:symmetry>1_555</PDBx:symmetry>
</PDBx:struct_site_gen>
</PDBx:struct_site_genCategory>
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
1
1
1
1
1
0
1
0
1
0
1
1
1
struct_site_genCategory
This property indicates that datablock
has a category element struct_site_gen.
struct_site_genItem
Abstract Datatype property for struct_site_gen items.
reference_to_struct_site_gen
cross-reference to struct_site_gen
struct_site_gen.auth_asym_id
A component of the identifier for participants in the site.
This data item is a pointer to attribute auth_asym_id in category atom_site in the
ATOM_SITE category.
struct_site_gen.auth_atom_id
A component of the identifier for participants in the site.
This data item is a pointer to attribute auth_atom_id in category atom_site in the
ATOM_SITE category.
struct_site_gen.auth_comp_id
A component of the identifier for participants in the site.
This data item is a pointer to attribute auth_comp_id in category atom_site in the
ATOM_SITE category.
struct_site_gen.auth_seq_id
A component of the identifier for participants in the site.
This data item is a pointer to attribute auth_seq_id in category atom_site in the
ATOM_SITE category.
struct_site_gen.details
A description of special aspects of the symmetry generation of
this portion of the structural site.
The zinc atom lies on a special position;
application of symmetry elements to generate
the insulin hexamer will generate excess zinc
atoms, which must be removed by hand.
struct_site_gen.label_alt_id
A component of the identifier for participants in the site.
This data item is a pointer to attribute id in category atom_sites_alt in the
ATOM_SITES_ALT category.
struct_site_gen.label_asym_id
A component of the identifier for participants in the site.
This data item is a pointer to attribute label_asym_id in category atom_site in the
ATOM_SITE category.
struct_site_gen.label_atom_id
A component of the identifier for participants in the site.
This data item is a pointer to attribute atom_id in category chem_comp_atom in the
CHEM_COMP_ATOM category.
struct_site_gen.label_comp_id
A component of the identifier for participants in the site.
This data item is a pointer to attribute label_comp_id in category atom_site in the
ATOM_SITE category.
struct_site_gen.label_seq_id
A component of the identifier for participants in the site.
This data item is a pointer to attribute label_seq_id in category atom_site in the
ATOM_SITE category.
struct_site_gen.pdbx_auth_ins_code
PDB insertion code.
struct_site_gen.pdbx_num_res
Number of residues in the site.
struct_site_gen.symmetry
Describes the symmetry operation that should be applied to the
atom set specified by attribute label* in category struct_site_gen to generate a
portion of the site.
4th symmetry operation applied
4
7th symm. posn.; +a on x; -b on y
7_645
struct_site_gen.id
The value of attribute id in category struct_site_gen must uniquely identify a record
in the STRUCT_SITE_GEN list.
Note that this item need not be a number; it can be any unique
identifier.
struct_site_gen.site_id
This data item is a pointer to attribute id in category struct_site in the STRUCT_SITE
category.
struct_site_keywords
Data items in the STRUCT_SITE_KEYWORDS category record
keywords describing the site.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:struct_site_keywordsCategory>
<PDBx:struct_site_keywords site_id="P2 site C" text="binding site"></PDBx:struct_site_keywords>
<PDBx:struct_site_keywords site_id="P2 site C" text="binding pocket"></PDBx:struct_site_keywords>
<PDBx:struct_site_keywords site_id="P2 site C" text="P2 site"></PDBx:struct_site_keywords>
<PDBx:struct_site_keywords site_id="P2 site C" text="P2 pocket"></PDBx:struct_site_keywords>
<PDBx:struct_site_keywords site_id="P2 site D" text="binding site"></PDBx:struct_site_keywords>
<PDBx:struct_site_keywords site_id="P2 site D" text="binding pocket"></PDBx:struct_site_keywords>
<PDBx:struct_site_keywords site_id="P2 site D" text="P2 site"></PDBx:struct_site_keywords>
<PDBx:struct_site_keywords site_id="P2 site D" text="P2 pocket"></PDBx:struct_site_keywords>
</PDBx:struct_site_keywordsCategory>
1
1
struct_site_keywordsCategory
This property indicates that datablock
has a category element struct_site_keywords.
struct_site_keywordsItem
Abstract Datatype property for struct_site_keywords items.
reference_to_struct_site_keywords
cross-reference to struct_site_keywords
struct_site_keywords.site_id
This data item is a pointer to attribute id in category struct_site in the STRUCT_SITE
category.
struct_site_keywords.text
Keywords describing this site.
active site
binding pocket
Ca coordination
struct_site_view
Data items in the STRUCT_SITE_VIEW category record details
about how to draw and annotate an informative view of the
site.
Example 1 - based on NDB structure GDL001 by Coll, Aymami,
Van Der Marel, Van Boom, Rich & Wang
[Biochemistry (1989), 28, 310-320].
<PDBx:struct_site_viewCategory>
<PDBx:struct_site_view id="1">
<PDBx:details> This view highlights the site of ATAT-Netropsin
interaction.</PDBx:details>
<PDBx:rot_matrix11>0.132</PDBx:rot_matrix11>
<PDBx:rot_matrix12>0.922</PDBx:rot_matrix12>
<PDBx:rot_matrix13>-0.363</PDBx:rot_matrix13>
<PDBx:rot_matrix21>0.131</PDBx:rot_matrix21>
<PDBx:rot_matrix22>-0.380</PDBx:rot_matrix22>
<PDBx:rot_matrix23>-0.916</PDBx:rot_matrix23>
<PDBx:rot_matrix31>-0.982</PDBx:rot_matrix31>
<PDBx:rot_matrix32>0.073</PDBx:rot_matrix32>
<PDBx:rot_matrix33>-0.172</PDBx:rot_matrix33>
</PDBx:struct_site_view>
</PDBx:struct_site_viewCategory>
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
1
struct_site_viewCategory
This property indicates that datablock
has a category element struct_site_view.
struct_site_viewItem
Abstract Datatype property for struct_site_view items.
reference_to_struct_site_view
cross-reference to struct_site_view
struct_site_view.details
A description of special aspects of this view of the
site. This data item can be used as a figure legend.
The active site has been oriented with the
specificity pocket on the right and the active
site machinery on the left.
struct_site_view.rot_matrix11
The [1][1] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_SITE_GEN category to an orientation useful for
visualizing the site. The conventions used in the rotation are
described in attribute details.
in category struct_site_view
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
struct_site_view.rot_matrix12
The [1][2] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_SITE_GEN category to an orientation useful for
visualizing the site. The conventions used in the rotation are
described in attribute details.
in category struct_site_view
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
struct_site_view.rot_matrix13
The [1][3] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_SITE_GEN category to an orientation useful for
visualizing the site. The conventions used in the rotation are
described in attribute details.
in category struct_site_view
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
struct_site_view.rot_matrix21
The [2][1] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_SITE_GEN category to an orientation useful for
visualizing the site. The conventions used in the rotation are
described in attribute details.
in category struct_site_view
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
struct_site_view.rot_matrix22
The [2][2] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_SITE_GEN category to an orientation useful for
visualizing the site. The conventions used in the rotation are
described in attribute details.
in category struct_site_view
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
struct_site_view.rot_matrix23
The [2][3] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_SITE_GEN category to an orientation useful for
visualizing the site. The conventions used in the rotation are
described in attribute details.
in category struct_site_view
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
struct_site_view.rot_matrix31
The [3][1] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_SITE_GEN category to an orientation useful for
visualizing the site. The conventions used in the rotation are
described in attribute details.
in category struct_site_view
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
struct_site_view.rot_matrix32
The [3][2] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_SITE_GEN category to an orientation useful for
visualizing the site. The conventions used in the rotation are
described in attribute details.
in category struct_site_view
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
struct_site_view.rot_matrix33
The [3][3] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_SITE_GEN category an orientation useful for visualizing
the site. The conventions used in the rotation are
described in attribute details.
in category struct_site_view
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
struct_site_view.site_id
This data item is a pointer to attribute id in category struct_site in the STRUCT_SITE
category.
struct_site_view.id
The value of attribute id in category struct_site_view must uniquely identify a
record in the STRUCT_SITE_VIEW list.
Note that this item need not be a number; it can be any unique
identifier.
Figure 1
unliganded enzyme
view down enzyme active site
symmetry
Data items in the SYMMETRY category record details about the
space-group symmetry.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:symmetryCategory>
<PDBx:symmetry entry_id="5HVP">
<PDBx:Int_Tables_number>18</PDBx:Int_Tables_number>
<PDBx:cell_setting>orthorhombic</PDBx:cell_setting>
<PDBx:space_group_name_H-M>P 21 21 2</PDBx:space_group_name_H-M>
</PDBx:symmetry>
</PDBx:symmetryCategory>
0
1
0
1
0
1
0
1
0
1
1
symmetryCategory
This property indicates that datablock
has a category element symmetry.
symmetryItem
Abstract Datatype property for symmetry items.
reference_to_symmetry
cross-reference to symmetry
symmetry.Int_Tables_number
Space-group number from International Tables for Crystallography
Vol. A (2002).
triclinic
monoclinic
orthorhombic
tetragonal
rhombohedral
trigonal
hexagonal
cubic
The cell settings for this space-group symmetry.
symmetry.pdbx_full_space_group_name_H-M
Used for PDB space group:
Example: 'C 1 2 1' (instead of C 2)
'P 1 2 1' (instead of P 2)
'P 1 21 1' (instead of P 21)
'P 1 1 21' (instead of P 21 -unique C axis)
'H 3' (instead of R 3 -hexagonal)
'H 3 2' (instead of R 3 2 -hexagonal)
Example: 'C 1 2 1' (instead of C 2)
'P 1 2 1' (instead of P 2)
'P 1 21 1' (instead of P 21)
'P 1 1 21' (instead of P 21 -unique C axis)
'H 3' (instead of R 3 -hexagonal)
'H 3 2' (instead of R 3 2 -hexagonal)
symmetry.space_group_name_H-M
Hermann-Mauguin space-group symbol. Note that the
Hermann-Mauguin symbol does not necessarily contain complete
information about the symmetry and the space-group origin. If
used, always supply the FULL symbol from International Tables
for Crystallography Vol. A (2002) and indicate the origin and
the setting if it is not implicit. If there is any doubt that
the equivalent positions can be uniquely deduced from this
symbol, specify the attribute pos_as_xyz in category symmetry_equiv or
attribute space_group_name_Hall in category symmetry data items as well. Leave
spaces between symbols referring to
different axes.
P 1 21/m 1
P 2/n 2/n 2/n (origin at -1)
R -3 2/m
symmetry.space_group_name_Hall
Space-group symbol as described by Hall (1981). This symbol
gives the space-group setting explicitly. Leave spaces between
the separate components of the symbol.
Ref: Hall, S. R. (1981). Acta Cryst. A37, 517-525; erratum
(1981) A37, 921.
-P 2ac 2n
-R 3 2"
P 61 2 2 (0 0 -1)
symmetry.entry_id
This data item is a pointer to attribute id in category entry in the ENTRY category.
symmetry_equiv
Data items in the SYMMETRY_EQUIV category list the
symmetry-equivalent positions for the space group.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<PDBx:symmetry_equivCategory>
<PDBx:symmetry_equiv id="1">
<PDBx:pos_as_xyz>+x,+y,+z</PDBx:pos_as_xyz>
</PDBx:symmetry_equiv>
<PDBx:symmetry_equiv id="2">
<PDBx:pos_as_xyz>-x,-y,z</PDBx:pos_as_xyz>
</PDBx:symmetry_equiv>
<PDBx:symmetry_equiv id="3">
<PDBx:pos_as_xyz>1/2+x,1/2-y,-z</PDBx:pos_as_xyz>
</PDBx:symmetry_equiv>
<PDBx:symmetry_equiv id="4">
<PDBx:pos_as_xyz>1/2-x,1/2+y,-z</PDBx:pos_as_xyz>
</PDBx:symmetry_equiv>
</PDBx:symmetry_equivCategory>
0
1
1
symmetry_equivCategory
This property indicates that datablock
has a category element symmetry_equiv.
symmetry_equivItem
Abstract Datatype property for symmetry_equiv items.
reference_to_symmetry_equiv
cross-reference to symmetry_equiv
symmetry_equiv.pos_as_xyz
Symmetry-equivalent position in the 'xyz' representation. Except
for the space group P1, these data will be repeated in a loop.
The format of the data item is as per International Tables for
Crystallography Vol. A (2002). All equivalent positions should
be entered, including those for lattice centring and a centre of
symmetry, if present.
-y+x,-y,1/3+z
symmetry_equiv.id
The value of attribute id in category symmetry_equiv must uniquely identify
a record in the SYMMETRY_EQUIV category.
Note that this item need not be a number; it can be any unique
identifier.
valence_param
Data items in the VALENCE_PARAM category define the
parameters used for calculating bond valences from bond
lengths. In addition to the parameters, a pointer
is given to the reference (in VALENCE_REF) from which
the bond-valence parameters were taken.
Example 1 - a bond-valence parameter list with accompanying references.
<PDBx:valence_paramCategory>
<PDBx:valence_param atom_1="Cu" atom_1_valence="2" atom_2="O" atom_2_valence="-2">
<PDBx:B>0.37</PDBx:B>
<PDBx:Ro>1.679</PDBx:Ro>
<PDBx:details></PDBx:details>
<PDBx:ref_id>a</PDBx:ref_id>
</PDBx:valence_param>
<PDBx:valence_param atom_1="Cu" atom_1_valence="2" atom_2="O" atom_2_valence="-2">
<PDBx:B>0.37</PDBx:B>
<PDBx:Ro>1.649</PDBx:Ro>
<PDBx:details></PDBx:details>
<PDBx:ref_id>j</PDBx:ref_id>
</PDBx:valence_param>
<PDBx:valence_param atom_1="Cu" atom_1_valence="2" atom_2="N" atom_2_valence="-3">
<PDBx:B>0.37</PDBx:B>
<PDBx:Ro>1.64</PDBx:Ro>
<PDBx:details>2-coordinate N</PDBx:details>
<PDBx:ref_id>m</PDBx:ref_id>
</PDBx:valence_param>
<PDBx:valence_param atom_1="Cu" atom_1_valence="2" atom_2="N" atom_2_valence="-3">
<PDBx:B>0.37</PDBx:B>
<PDBx:Ro>1.76</PDBx:Ro>
<PDBx:details>3-coordinate N</PDBx:details>
<PDBx:ref_id>m</PDBx:ref_id>
</PDBx:valence_param>
</PDBx:valence_paramCategory>
<PDBx:valence_refCategory>
<PDBx:valence_ref id="a">
<PDBx:reference>Brown & Altermatt (1985), Acta Cryst. B41, 244-247</PDBx:reference>
</PDBx:valence_ref>
<PDBx:valence_ref id="j">
<PDBx:reference>Liu & Thorp (1993), Inorg. Chem. 32, 4102-4205</PDBx:reference>
</PDBx:valence_ref>
<PDBx:valence_ref id="m">
<PDBx:reference>See, Krause & Strub (1998), Inorg. Chem. 37, 5369-5375</PDBx:reference>
</PDBx:valence_ref>
</PDBx:valence_refCategory>
0
1
0
1
0
1
0
1
0
1
1
1
1
1
valence_paramCategory
This property indicates that datablock
has a category element valence_param.
valence_paramItem
Abstract Datatype property for valence_param items.
reference_to_valence_param
cross-reference to valence_param
valence_param.B
The bond-valence parameter B used in the expression
s = exp[(Ro - R)/B]
where s is the valence of a bond of length R.
valence_param.Ro
The bond-valence parameter Ro used in the expression
s = exp[(Ro - R)/B]
where s is the valence of a bond of length R.
valence_param.details
Details of or comments on the bond-valence parameters.
valence_param.id
An identifier for the valence parameters of a bond between
the given atoms.
valence_param.ref_id
An identifier which links to the reference to the source
from which the bond-valence parameters are taken. A child
of attribute id in category valence_ref which it must match.
valence_param.atom_1
The element symbol of the first atom forming the bond whose
bond-valence parameters are given in this category.
valence_param.atom_1_valence
The valence (formal charge) of the first atom whose
bond-valence parameters are given in this category.
valence_param.atom_2
The element symbol of the second atom forming the bond whose
bond-valence parameters are given in this category.
valence_param.atom_2_valence
The valence (formal charge) of the second atom whose
bond-valence parameters are given in this category.
valence_ref
Data items in the VALENCE_REF category list the references
from which the bond-valence parameters have been taken.
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valence_refCategory
This property indicates that datablock
has a category element valence_ref.
valence_refItem
Abstract Datatype property for valence_ref items.
reference_to_valence_ref
cross-reference to valence_ref
valence_ref.reference
Literature reference from which the valence parameters
identified by attribute id in category valence_param were taken.
valence_ref.id
An identifier for items in this category. Parent of
attribute ref_id in category valence_param, which must have the same value.