The PDBx OWL ontology translated from the PDBML schema.
Abstract Datatype property for category items
Abstract property for cross-references between categories.
external link to DOI (digital object identifier)
external link to NCBI taxonomy (source organism)
external link to NCBI taxonomy (host organism)
DATABLOCK class holds all categories of PDB data.
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>
This property indicates that datablock has a category element atom_site.
Abstract Datatype property for atom_site items.
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.
The standard uncertainty (estimated standard deviation) of attribute B_equiv_geom_mean in category atom_site.
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.
The standard uncertainty (estimated standard deviation) of attribute B_iso_or_equiv in category atom_site.
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.
The standard uncertainty (estimated standard deviation) of attribute Cartn_x in category atom_site.
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.
The standard uncertainty (estimated standard deviation) of attribute Cartn_y in category atom_site.
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.
The standard uncertainty (estimated standard deviation) of attribute Cartn_z in category atom_site.
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^
The standard uncertainty (estimated standard deviation) of attribute U_equiv_geom_mean in category atom_site.
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.
The standard uncertainty (estimated standard deviation) of attribute U_iso_or_equiv in category atom_site.
The Wyckoff symbol (letter) as listed in the space-group tables of International Tables for Crystallography, Vol. A (2002).
A standard code used to describe the type of atomic displacement parameters used for the site.
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.
The standard uncertainty (estimated standard deviation) of attribute aniso_B[1][1] in category atom_site.
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.
The standard uncertainty (estimated standard deviation) of attribute aniso_B[1][2] in category atom_site.
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.
The standard uncertainty (estimated standard deviation) of attribute aniso_B[1][3] in category atom_site.
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.
The standard uncertainty (estimated standard deviation) of attribute aniso_B[2][2] in category atom_site.
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.
The standard uncertainty (estimated standard deviation) of attribute aniso_B[2][3] in category atom_site.
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.
The standard uncertainty (estimated standard deviation) of attribute aniso_B[3][3] in category atom_site.
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.
The standard uncertainty (estimated standard deviation) of attribute aniso_U[1][1] in category atom_site.
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.
The standard uncertainty (estimated standard deviation) of attribute aniso_U[1][2] in category atom_site.
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.
The standard uncertainty (estimated standard deviation) of attribute aniso_U[1][3] in category atom_site.
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.
The standard uncertainty (estimated standard deviation) of attribute aniso_U[2][2] in category atom_site.
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.
The standard uncertainty (estimated standard deviation) of attribute aniso_U[2][3] in category atom_site.
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.
The standard uncertainty (estimated standard deviation) of attribute aniso_U[3][3] in category atom_site.
Ratio of the maximum to minimum principal axes of displacement (thermal) ellipsoids.
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
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.
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.
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.
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.
The attribute id in category atom_site of the atom site to which the 'geometry-calculated' atom site is attached.
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'.
This data item is a pointer to attribute number in category chemical_conn_atom in the CHEMICAL_CONN_ATOM category.
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)
A description of special aspects of this site. See also attribute refinement_flags in category atom_site. Ag/Si disordered
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. ***
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. ***
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.
The x coordinate of the atom-site position specified as a fraction of attribute length_a in category cell.
The standard uncertainty (estimated standard deviation) of attribute fract_x in category atom_site.
The y coordinate of the atom-site position specified as a fraction of attribute length_b in category cell.
The standard uncertainty (estimated standard deviation) of attribute fract_y in category atom_site.
The z coordinate of the atom-site position specified as a fraction of attribute length_c in category cell.
The standard uncertainty (estimated standard deviation) of attribute fract_z in category atom_site.
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.
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.
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.
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.
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.
This data item is a pointer to attribute id in category entity in the ENTITY category.
This data item is a pointer to attribute num in category entity_poly_seq in the ENTITY_POLY_SEQ category.
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.
The standard uncertainty (estimated standard deviation) of attribute occupancy in category atom_site.
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
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.
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.
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.
A code which indicates the refinement restraints or constraints applied to the atomic displacement parameters of this site.
A code which indicates that refinement restraints or constraints were applied to the occupancy of this site.
A code which indicates the refinement restraints or constraints applied to the positional coordinates of this site.
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
The multiplicity of a site due to the space-group symmetry as is given in International Tables for Crystallography Vol. A (2002).
This data item is a pointer to attribute symbol in category atom_type in the ATOM_TYPE category.
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
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>
This property indicates that datablock has a category element atom_site_anisotrop.
Abstract Datatype property for atom_site_anisotrop items.
The standard uncertainty (estimated standard deviation) of attribute B[1][1] in category atom_site_anisotrop.
The standard uncertainty (estimated standard deviation) of attribute B[1][2] in category atom_site_anisotrop.
The standard uncertainty (estimated standard deviation) of attribute B[1][3] in category atom_site_anisotrop.
The standard uncertainty (estimated standard deviation) of attribute B[2][2] in category atom_site_anisotrop.
The standard uncertainty (estimated standard deviation) of attribute B[2][3] in category atom_site_anisotrop.
The standard uncertainty (estimated standard deviation) of attribute B[3][3] in category atom_site_anisotrop.
The standard uncertainty (estimated standard deviation) of attribute U[1][1] in category atom_site_anisotrop.
The standard uncertainty (estimated standard deviation) of attribute U[1][2] in category atom_site_anisotrop.
The standard uncertainty (estimated standard deviation) of attribute U[1][3] in category atom_site_anisotrop.
The standard uncertainty (estimated standard deviation) of attribute U[2][2] in category atom_site_anisotrop.
The standard uncertainty (estimated standard deviation) of attribute U[2][3] in category atom_site_anisotrop.
The standard uncertainty (estimated standard deviation) of attribute U[3][3] in category atom_site_anisotrop.
Pointer to attribute pdbx_PDB_ins_code in category atom_site
Pointer to attribute pdbx_auth_alt_id in category atom_site.
Pointer to attribute auth_asym_id in category atom_site
Pointer to attribute auth_atom_id in category atom_site
Pointer to attribute auth_comp_id in category atom_site
Pointer to attribute auth_seq_id in category atom_site
Pointer to attribute label_alt_id in category atom_site.
Pointer to attribute label_asym_id in category atom_site
Pointer to attribute label_atom_id in category atom_site
Pointer to attribute label_comp_id in category atom_site
Pointer to attribute label_seq_id in category atom_site
This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category.
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>
This property indicates that datablock has a category element atom_sites.
Abstract Datatype property for atom_sites items.
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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. ***
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. ***
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. ***
Additional information about the atomic coordinates not coded elsewhere in the CIF.
This data item is a pointer to attribute id in category entry in the ENTRY category.
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>
This property indicates that datablock has a category element atom_sites_alt.
Abstract Datatype property for atom_sites_alt items.
A description of special aspects of the modelling of atoms in alternative conformations.
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
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>
This property indicates that datablock has a category element atom_sites_alt_ens.
Abstract Datatype property for atom_sites_alt_ens items.
A description of special aspects of the ensemble structure generated from atoms with various alternative IDs.
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.
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>
This property indicates that datablock has a category element atom_sites_alt_gen.
Abstract Datatype property for atom_sites_alt_gen items.
This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITES_ALT category.
This data item is a pointer to attribute id in category atom_sites_alt_ens in the ATOM_SITES_ALT_ENS category.
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>
This property indicates that datablock has a category element atom_sites_footnote.
Abstract Datatype property for atom_sites_footnote items.
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.
A code that identifies the footnote. a b 1 2
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>
This property indicates that datablock has a category element atom_type.
Abstract Datatype property for atom_type items.
Mass percentage of this atom type derived from chemical analysis.
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
Total number of atoms of this atom type in the unit cell.
Formal oxidation state of this atom type in the structure.
The effective intramolecular bonding radius in angstroms of this atom type.
The effective intermolecular bonding radius in angstroms of this atom type.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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
The bound coherent scattering length in femtometres for the atom type at the isotopic composition used for the diffraction experiment.
Reference to the source of the scattering factors or scattering lengths used for this atom type. International Tables Vol. IV Table 2.4.6B
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.
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
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>
This property indicates that datablock has a category element audit.
Abstract Datatype property for audit items.
A date that the data block was created. The date format is yyyy-mm-dd. 1990-07-12
A description of how data were entered into the data block. spawned by the program QBEE
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
The value of attribute revision_id in category audit must uniquely identify a record in the AUDIT list. rev1
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>
This property indicates that datablock has a category element audit_author.
Abstract Datatype property for audit_author items.
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
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
This data item defines the order of the author's name in the list of audit authors. 1 2 3
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>
This property indicates that datablock has a category element audit_conform.
Abstract Datatype property for audit_conform items.
A file name or uniform resource locator (URL) for the dictionary to which the current data block conforms.
The string identifying the highest-level dictionary defining data names used in this file.
The version number of the dictionary to which the current data block conforms.
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>
This property indicates that datablock has a category element audit_contact_author.
Abstract Datatype property for audit_contact_author items.
The mailing address of the author of the data block to whom correspondence should be addressed. Department Institute Street City and postcode COUNTRY
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
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
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
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
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>
This property indicates that datablock has a category element audit_link.
Abstract Datatype property for audit_link items.
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.
A textual description of the relationship of the referenced data block to the current one.
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>
This property indicates that datablock has a category element cell.
Abstract Datatype property for cell items.
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.
Unit-cell angle alpha of the reported structure in degrees.
The standard uncertainty (estimated standard deviation) of attribute angle_alpha in category cell.
Unit-cell angle beta of the reported structure in degrees.
The standard uncertainty (estimated standard deviation) of attribute angle_beta in category cell.
Unit-cell angle gamma of the reported structure in degrees.
The standard uncertainty (estimated standard deviation) of attribute angle_gamma in category cell.
A description of special aspects of the cell choice, noting possible alternative settings. pseudo-orthorhombic standard setting from 45 deg rotation around c
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.
Unit-cell length a corresponding to the structure reported in angstroms.
The standard uncertainty (estimated standard deviation) of attribute length_a in category cell.
Unit-cell length b corresponding to the structure reported in angstroms.
The standard uncertainty (estimated standard deviation) of attribute length_b in category cell.
Unit-cell length c corresponding to the structure reported in angstroms.
The standard uncertainty (estimated standard deviation) of attribute length_c in category cell.
To further identify unique axis if necessary. E.g., P 21 with an unique C axis will have 'C' in this field.
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.
The estimated standard deviation of attribute reciprocal_angle_alpha in category cell.
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.
The estimated standard deviation of attribute reciprocal_angle_beta in category cell.
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.
The estimated standard deviation of attribute reciprocal_angle_gamma in category cell.
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.
The estimated standard deviation of attribute reciprocal_length_a in category cell.
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.
The estimated standard deviation of attribute reciprocal_length_b in category cell.
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.
The estimated standard deviation of attribute reciprocal_length_c in category cell.
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
The standard uncertainty (estimated standard deviation) of attribute volume in category cell.
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>
This property indicates that datablock has a category element cell_measurement.
Abstract Datatype property for cell_measurement items.
The pressure in kilopascals at which the unit-cell parameters were measured (not the pressure at which the sample was synthesized).
The standard uncertainty (estimated standard deviation) of attribute pressure in category cell_measurement.
Description of the radiation used to measure the unit-cell data. See also attribute wavelength in category cell_measurement. neutron Cu K\a synchrotron
The total number of reflections used to determine the unit cell. These reflections may be specified as CELL_MEASUREMENT_REFLN data items.
The temperature in kelvins at which the unit-cell parameters were measured (not the temperature of synthesis).
The standard uncertainty (estimated standard deviation) of attribute temp in category cell_measurement.
The maximum theta angle of reflections used to measure the unit cell in degrees.
The minimum theta angle of reflections used to measure the unit cell in degrees.
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.
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>
This property indicates that datablock has a category element cell_measurement_refln.
Abstract Datatype property for cell_measurement_refln items.
cross-reference to cell_measurement_refln
Theta angle for a reflection used for measurement of the unit cell in degrees.
Miller index h of a reflection used for measurement of the unit cell.
Miller index k of a reflection used for measurement of the unit cell.
Miller index l of a reflection used for measurement of the unit cell.
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>
This property indicates that datablock has a category element chem_comp.
Abstract Datatype property for chem_comp items.
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
Formula mass in daltons of the chemical component.
A description of special aspects of the generation of the coordinates for the model of the component. geometry idealized but not minimized
A pointer to an external reference file from which the atomic description of the component is taken.
The source of the coordinates for the model of the component. CSD entry ABCDEF built using Quanta/Charmm
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
A description of special details of a nonstandard monomer.
'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.
The name of the parent monomer of the nonstandard monomer, if the nonstandard monomer represents a modification of a standard monomer. tyrosine cytosine
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.
The full name of the component. alanine valine adenine cytosine
The total number of atoms in the component.
The number of non-hydrogen atoms in the component.
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
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.
A serial number used by PDB in the FORMUL record. 3
The net integer charge assigned to this component. This is the formal charge assignment normally found in chemical diagrams.
This data item identifies the source of the ideal coordinates in the component definition.
This data item identifies if ideal coordinates are missing in this definition.
This data item identifies the PDB database code from which the heavy atom model coordinates were obtained.
This data item provides additional details about the model coordinates in the component definition.
This data item identifies if model coordinates are missing in this definition.
For nonstandard components a text description of modification of the parent component. ATP
This data item identifies the deposition site that processed this chemical component defintion.
This data item holds the current release status for the component.
Identifies the attribute id in category chem_comp of the component that has replaced this component. q11 tvx
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
The list of subcomponents contained in this component. TSM DPH HIS CHF EMR
A preliminary classification used by PDB.
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
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.
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
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>
This property indicates that datablock has a category element chem_comp_angle.
Abstract Datatype property for chem_comp_angle items.
The value that should be taken as the target value for the angle associated with the specified atoms, expressed in degrees.
The standard uncertainty (estimated standard deviation) of attribute value_angle in category chem_comp_angle.
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.
The standard uncertainty (estimated standard deviation) of attribute value_dist in category chem_comp_angle.
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.
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.
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.
This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category.
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>
This property indicates that datablock has a category element chem_comp_atom.
Abstract Datatype property for chem_comp_atom items.
An alternative identifier for the atom. This data item would be used in cases where alternative nomenclatures exist for labelling atoms in a group.
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.
The standard uncertainty (estimated standard deviation) of attribute model_Cartn_x in category chem_comp_atom.
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.
The standard uncertainty (estimated standard deviation) of attribute model_Cartn_y in category chem_comp_atom.
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.
The standard uncertainty (estimated standard deviation) of attribute model_Cartn_z in category chem_comp_atom.
The partial charge assigned to this atom.
Atom name alignment offset in PDB atom field.
The atom identifier in the subcomponent where a larger component has been divided subcomponents. CB CA CG
The component identifier for the subcomponent where a larger component has been divided subcomponents. HIS PRO
An alternative x component of the coordinates for this atom in this component specified as orthogonal angstroms.
An alternative y component of the coordinates for this atom in this component specified as orthogonal angstroms.
An alternative z component of the coordinates for this atom in this component specified as orthogonal angstroms.
Ordinal index for the component atom list.
The chiral configuration of the atom that is a chiral center.
This data item assigns the atom to a substructure of the component, if appropriate.
The code used to identify the atom species representing this atom type. Normally this code is the element symbol. C N O
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.
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>
This property indicates that datablock has a category element chem_comp_bond.
Abstract Datatype property for chem_comp_bond items.
Ordinal index for the component bond list.
Stereochemical configuration across a double bond.
The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a distance.
The standard uncertainty (estimated standard deviation) of attribute value_dist in category chem_comp_bond.
The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a bond order.
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.
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.
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>
This property indicates that datablock has a category element chem_comp_chir.
Abstract Datatype property for chem_comp_chir items.
The chiral configuration of the atom that is a chiral centre.
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.
The total number of atoms bonded to the atom specified by attribute atom_id in category chem_comp_chir.
The number of non-hydrogen atoms bonded to the atom specified by attribute atom_id in category chem_comp_chir.
A flag to indicate whether a chiral volume should match the standard value in both magnitude and sign, or in magnitude only.
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
The standard uncertainty (estimated standard deviation) of attribute volume_three in category chem_comp_chir.
The value of attribute id in category chem_comp_chir must uniquely identify a record in the CHEM_COMP_CHIR list.
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>
This property indicates that datablock has a category element chem_comp_chir_atom.
Abstract Datatype property for chem_comp_chir_atom items.
The standard uncertainty (estimated standard deviation) of the position of this atom from the plane defined by all of the atoms in the plane.
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.
This data item is a pointer to attribute id in category chem_comp_chir in the CHEM_COMP_CHIR category.
Data items in the CHEM_COMP_LINK category give details about the links between chemical components.
This property indicates that datablock has a category element chem_comp_link.
Abstract Datatype property for chem_comp_link items.
A description of special aspects of a link between chemical components in the structure.
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.
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.
This data item is a pointer to attribute id in category chem_link in the CHEM_LINK category.
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>
This property indicates that datablock has a category element chem_comp_plane.
Abstract Datatype property for chem_comp_plane items.
The number of non-hydrogen atoms in the plane.
The value of attribute id in category chem_comp_plane must uniquely identify a record in the CHEM_COMP_PLANE list.
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>
This property indicates that datablock has a category element chem_comp_plane_atom.
Abstract Datatype property for chem_comp_plane_atom items.
This data item is the standard deviation of the out-of-plane distance for this atom.
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.
This data item is a pointer to attribute id in category chem_comp_plane in the CHEM_COMP_PLANE category.
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>
This property indicates that datablock has a category element chem_comp_tor.
Abstract Datatype property for chem_comp_tor items.
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.
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.
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.
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.
The value of attribute id in category chem_comp_tor must uniquely identify a record in the CHEM_COMP_TOR list.
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>
This property indicates that datablock has a category element chem_comp_tor_value.
Abstract Datatype property for chem_comp_tor_value items.
A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed in degrees.
The standard uncertainty (estimated standard deviation) of attribute angle in category chem_comp_tor_value.
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.
The standard uncertainty (estimated standard deviation) of attribute dist in category chem_comp_tor_value.
This data item is a pointer to attribute comp_id in category chem_comp_atom in the CHEM_COMP_ATOM category.
This data item is a pointer to attribute id in category chem_comp_tor in the CHEM_COMP_TOR category.
Data items in the CHEM_LINK category give details about the links between chemical components.
This property indicates that datablock has a category element chem_link.
Abstract Datatype property for chem_link items.
The value of attribute id in category chem_link must uniquely identify each item in the CHEM_LINK list. peptide oligosaccharide 1,4 DNA
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>
This property indicates that datablock has a category element chem_link_angle.
Abstract Datatype property for chem_link_angle items.
This data item indicates whether atom 1 is found in the first or the second of the two components connected by the link.
This data item indicates whether atom 2 is found in the first or the second of the two components connected by the link.
This data item indicates whether atom 3 is found in the first or the second of the two components connected by the link.
The standard uncertainty (estimated standard deviation) of attribute value_angle in category chem_link_angle.
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.
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.
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.
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>
This property indicates that datablock has a category element chem_link_bond.
Abstract Datatype property for chem_link_bond items.
This data item indicates whether atom 2 is found in the first or the second of the two chemical components connected by the link.
The standard uncertainty (estimated standard deviation) of attribute value_dist in category chem_link_bond.
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.
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.
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.
This property indicates that datablock has a category element chem_link_chir.
Abstract Datatype property for chem_link_chir items.
This data item indicates whether the chiral atom is found in the first or the second of the two components connected by the link.
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.
The total number of atoms bonded to the atom specified by attribute atom_id in category chem_link_chir.
The number of non-hydrogen atoms bonded to the atom specified by attribute atom_id in category chem_link_chir.
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
The standard uncertainty (estimated standard deviation) of attribute volume_three in category chem_link_chir.
The value of attribute id in category chem_link_chir must uniquely identify a record in the CHEM_LINK_CHIR list.
Data items in the CHEM_LINK_CHIR_ATOM category enumerate the atoms bonded to a chiral atom in a link between two chemical components.
This property indicates that datablock has a category element chem_link_chir_atom.
Abstract Datatype property for chem_link_chir_atom items.
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.
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.
This data item is a pointer to attribute id in category chem_link_chir in the CHEM_LINK_CHIR category.
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.
This property indicates that datablock has a category element chem_link_plane.
Abstract Datatype property for chem_link_plane items.
The value of attribute id in category chem_link_plane must uniquely identify a record in the CHEM_LINK_PLANE list.
Data items in the CHEM_LINK_PLANE_ATOM category enumerate the atoms in a plane in a link between two chemical components.
This property indicates that datablock has a category element chem_link_plane_atom.
Abstract Datatype property for chem_link_plane_atom items.
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.
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.
This data item is a pointer to attribute id in category chem_link_plane in the CHEM_LINK_PLANE category.
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.
This property indicates that datablock has a category element chem_link_tor.
Abstract Datatype property for chem_link_tor items.
This data item indicates whether atom 4 is found in the first or the second of the two components connected by the link.
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.
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.
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.
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.
The value of attribute id in category chem_link_tor must uniquely identify a record in the CHEM_LINK_TOR list.
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.
This property indicates that datablock has a category element chem_link_tor_value.
Abstract Datatype property for chem_link_tor_value items.
The standard uncertainty (estimated standard deviation) of attribute angle in category chem_link_tor_value.
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.
The standard uncertainty (estimated standard deviation) of attribute dist in category chem_link_tor_value.
This data item is a pointer to attribute id in category chem_link_tor in the CHEM_LINK_TOR category.
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>
This property indicates that datablock has a category element chemical.
Abstract Datatype property for chemical items.
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)
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
The temperature in kelvins at which the crystalline solid changes to a liquid.
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.
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.
Trivial name by which the compound is commonly known. 1-bromoestradiol
Mineral name accepted by the International Mineralogical Association. Use only for natural minerals. See also attribute compound_source in category chemical. chalcopyrite
Commonly used structure-type name. Usually only applied to minerals or inorganic compounds. perovskite sphalerite A15
IUPAC or Chemical Abstracts full name of the compound. 1-bromoestra-1,3,5(10)-triene-3,17\b-diol
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~)
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
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
The temperature in kelvins at which the solid decomposes. 350
The estimated standard deviation of attribute temperature_decomposition in category chemical.
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
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
The temperature in kelvins at which the solid sublimes. 350
The estimated standard deviation of attribute temperature_sublimation in category chemical.
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
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
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>
This property indicates that datablock has a category element chemical_conn_atom.
Abstract Datatype property for chemical_conn_atom items.
The number of connected atoms excluding terminal hydrogen atoms.
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.
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.
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.
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.
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>
This property indicates that datablock has a category element chemical_conn_bond.
Abstract Datatype property for chemical_conn_bond items.
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.
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>
This property indicates that datablock has a category element chemical_formula.
Abstract Datatype property for chemical_formula items.
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
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
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)
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
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
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.
Formula mass in daltons measured by a non-diffraction experiment.
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>
This property indicates that datablock has a category element citation.
Abstract Datatype property for citation items.
Abstract for the citation. This is used most when the citation is extracted from a bibliographic database that contains full text or abstract information.
The Chemical Abstracts Service (CAS) abstract identifier; relevant for journal articles.
The International Standard Book Number (ISBN) code assigned to the book cited; relevant for books or book chapters.
The name of the publisher of the citation; relevant for books or book chapters. John Wiley and Sons
The location of the publisher of the citation; relevant for books or book chapters. London
The title of the book in which the citation appeared; relevant for books or book chapters.
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'.
The country of publication; relevant for books and book chapters.
Identifier ('refcode') of the database record in the Cambridge Structural Database that contains details of the cited structure. LEKKUH
Accession number used by Medline to categorize a specific bibliographic entry. 89064067
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
Abbreviated name of the cited journal as given in the Chemical Abstracts Service Source Index. J. Mol. Biol.
Full name of the cited journal; relevant for journal articles. Journal of Molecular Biology
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.
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
The International Standard Serial Number (ISSN) code assigned to the journal cited; relevant for journal articles.
Issue number of the journal cited; relevant for journal articles. 2
Volume number of the journal cited; relevant for journal articles. 174
Language in which the cited article is written. German
The first page of the citation; relevant for journal articles, books and book chapters.
The last page of the citation; relevant for journal articles, books and book chapters.
Document Object Identifier used by doi.org to uniquely specify bibliographic entry. DOI:10.2345/S1384107697000225
Ascession number used by PubMed to categorize a specific bibliographic entry. 12627512
The title of the citation; relevant for journal articles, books and book chapters. Structure of diferric duck ovotransferrin at 2.35 \%A resolution.
Flag to indicate that this citation will not be published.
The year of the citation; relevant for journal articles, books and book chapters. 1984
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
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>
This property indicates that datablock has a category element citation_author.
Abstract Datatype property for citation_author items.
This data item is a pointer to attribute id in category citation in the CITATION category.
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
This data item defines the order of the author's name in the list of authors of a citation.
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>
This property indicates that datablock has a category element citation_editor.
Abstract Datatype property for citation_editor items.
This data item defines the order of the editor's name in the list of editors of a citation.
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
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>
This property indicates that datablock has a category element computing.
Abstract Datatype property for computing items.
Software used for cell refinement. Give the program or package name and a brief reference. CAD4 (Enraf-Nonius, 1989)
Software used for data collection. Give the program or package name and a brief reference. CAD4 (Enraf-Nonius, 1989)
Software used for data reduction. Give the program or package name and a brief reference. DIFDAT, SORTRF, ADDREF (Hall & Stewart, 1990)
Software used for molecular graphics. Give the program or package name and a brief reference. FRODO (Jones, 1986), ORTEP (Johnson, 1965)
Program/package name for data reduction/data scaling
Program/package name for data reduction/intensity integration software
Program/package name for structure refinement method.
Software used for generating material for publication. Give the program or package name and a brief reference.
Software used for refinement of the structure. Give the program or package name and a brief reference. SHELX85 (Sheldrick, 1985) X-PLOR (Brunger, 1992)
Software used for solution of the structure. Give the program or package name and a brief reference. SHELX85 (Sheldrick, 1985)
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.
This property indicates that datablock has a category element database.
Abstract Datatype property for database items.
A history of changes made by the Cambridge Crystallographic Data Centre and incorporated into the Cambridge Structural Database (CSD).
The code assigned by Chemical Abstracts.
The code assigned by the Cambridge Structural Database.
The code assigned by the Inorganic Crystal Structure Database.
The code assigned by the Metals Data File.
The code assigned by the NBS (NIST) Crystal Data Database.
The code assigned by the Protein Data Bank.
The code assigned by the Powder Diffraction File (JCPDS/ICDD).
Deposition numbers assigned by the Cambridge Crystallographic Data Centre (CCDC) to files containing structural information archived by the CCDC.
Deposition numbers assigned by the Fachinformationszentrum Karlsruhe (FIZ) to files containing structural information archived by the Cambridge Crystallographic Data Centre (CCDC).
Deposition numbers assigned by various journals to files containing structural information archived by the Cambridge Crystallographic Data Centre (CCDC).
The ASTM CODEN designator for a journal as given in the Chemical Source List maintained by the Chemical Abstracts Service.
The journal code used in the Cambridge Structural Database.
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>
This property indicates that datablock has a category element database_2.
Abstract Datatype property for database_2 items.
The code assigned by the database identified in attribute database_id in category database_2. 1ABC ABCDEF
An abbreviation that identifies the database.
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>
This property indicates that datablock has a category element database_PDB_caveat.
Abstract Datatype property for database_PDB_caveat items.
A unique identifier for the PDB caveat record.
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.
This property indicates that datablock has a category element database_PDB_matrix.
Abstract Datatype property for database_PDB_matrix items.
The [1][1] element of the PDB ORIGX matrix.
The [1][2] element of the PDB ORIGX matrix.
The [1][3] element of the PDB ORIGX matrix.
The [2][1] element of the PDB ORIGX matrix.
The [2][2] element of the PDB ORIGX matrix.
The [2][3] element of the PDB ORIGX matrix.
The [3][1] element of the PDB ORIGX matrix.
The [3][2] element of the PDB ORIGX matrix.
The [3][3] element of the PDB ORIGX matrix.
The [1] element of the PDB ORIGX vector.
The [2] element of the PDB ORIGX vector.
The [3] element of the PDB ORIGX vector.
The [1][1] element of the PDB SCALE matrix.
The [1][2] element of the PDB SCALE matrix.
The [1][3] element of the PDB SCALE matrix.
The [2][1] element of the PDB SCALE matrix.
The [2][2] element of the PDB SCALE matrix.
The [2][3] element of the PDB SCALE matrix.
The [3][1] element of the PDB SCALE matrix.
The [3][2] element of the PDB SCALE matrix.
The [3][3] element of the PDB SCALE matrix.
The [1] element of the PDB SCALE vector.
The [2] element of the PDB SCALE vector.
The [3] element of the PDB SCALE vector.
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>
This property indicates that datablock has a category element database_PDB_remark.
Abstract Datatype property for database_PDB_remark items.
A unique identifier for the PDB remark record.
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>
This property indicates that datablock has a category element database_PDB_rev.
Abstract Datatype property for database_PDB_rev items.
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
Date the PDB revision took place. Taken from the REVDAT record.
Date the entry first entered the PDB database in the form yyyy-mm-dd. Taken from the PDB HEADER record. 1980-08-21
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.
The PDB code for a subsequent PDB entry that replaced the PDB file corresponding to this data block.
The PDB code for a previous PDB entry that was replaced by the PDB file corresponding to this data block.
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.
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>
This property indicates that datablock has a category element database_PDB_rev_record.
Abstract Datatype property for database_PDB_rev_record items.
cross-reference to database_PDB_rev_record
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
This data item is a pointer to attribute num in category database_PDB_rev in the DATABASE_PDB_REV category.
The types of records that were changed in this revision to a PDB entry. CRYST1 SCALE MTRIX ATOM HETATM
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.
This property indicates that datablock has a category element database_PDB_tvect.
Abstract Datatype property for database_PDB_tvect items.
A description of special aspects of this TVECT.
The [1] element of the PDB TVECT vector.
The [2] element of the PDB TVECT vector.
The [3] element of the PDB TVECT vector.
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.
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>
This property indicates that datablock has a category element diffrn.
Abstract Datatype property for diffrn items.
The gas or liquid surrounding the sample, if not air.
The mean hydrostatic pressure in kilopascals at which the intensities were measured.
The estimated standard deviation of attribute ambient_pressure in category diffrn.
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.
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.
The mean temperature in kelvins at which the intensities were measured.
A description of special aspects of temperature control during data collection.
The standard uncertainty (estimated standard deviation) of attribute ambient_temp in category diffrn.
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.
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.
This data item is a pointer to attribute id in category exptl_crystal in the EXPTL_CRYSTAL category.
The physical device used to support the crystal during data collection. glass capillary quartz capillary fiber metal loop
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
Special details of the diffraction measurement process. Should include information about source instability, crystal motion, degradation and so on.
This data item uniquely identifies a set of diffraction data.
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>
This property indicates that datablock has a category element diffrn_attenuator.
Abstract Datatype property for diffrn_attenuator items.
Material from which the attenuator is made.
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.
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.
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>
This property indicates that datablock has a category element diffrn_detector.
Abstract Datatype property for diffrn_detector items.
The resolution of an area detector, in pixels/mm.
A description of special aspects of the radiation detector.
The general class of the radiation detector. photographic film scintillation counter CCD plate BF~3~ counter
The deadtime in microseconds of the detector used to measure the diffraction intensities.
The date of data collection. 1996-12-25
The total number of seconds required to measure this data set. 120.0
The total number of data frames collected for this data set. 20 100
The make, model or name of the detector device used.
This data item is a pointer to attribute id in category diffrn in the DIFFRN category.
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>
This property indicates that datablock has a category element diffrn_measurement.
Abstract Datatype property for diffrn_measurement items.
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
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
A description of special aspects of the device used to measure the diffraction intensities. commercial goniometer modified locally to allow for 90\% \t arc
The make, model or name of the measurement device (goniometer) used. Supper model q Huber model r Enraf-Nonius model s homemade
Method used to measure intensities. profile data from theta/2theta scans
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>
This property indicates that datablock has a category element diffrn_orient_matrix.
Abstract Datatype property for diffrn_orient_matrix items.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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>
This property indicates that datablock has a category element diffrn_orient_refln.
Abstract Datatype property for diffrn_orient_refln items.
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.
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.
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.
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.
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.
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.
Miller index h of a reflection used to define the orientation matrix.
Miller index k of a reflection used to define the orientation matrix.
Miller index l of a reflection used to define the orientation matrix.
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>
This property indicates that datablock has a category element diffrn_radiation.
Abstract Datatype property for diffrn_radiation items.
The collimation or focusing applied to the radiation. 0.3 mm double-pinhole 0.5 mm focusing mirrors
Absorption edge in angstroms of the radiation filter used.
Half-width in millimetres of the incident beam in the direction perpendicular to the diffraction plane.
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
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
SINGLE WAVELENGTH, LAUE, or MAD. SINGLE WAVELENGTH MONOCHROMATIC LAUE MAD OTHER
Comma separated list of wavelengths or wavelength range.
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.
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).
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.
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
This data item is a pointer to attribute id in category diffrn_radiation_wavelength in the DIFFRN_RADIATION_WAVELENGTH category.
The IUPAC symbol for the X-ray wavelength for the probe radiation.
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>
This property indicates that datablock has a category element diffrn_radiation_wavelength.
Abstract Datatype property for diffrn_radiation_wavelength items.
cross-reference to diffrn_radiation_wavelength
The relative weight of a wavelength identified by the code attribute id in category diffrn_radiation_wavelength in the list of wavelengths.
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
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>
This property indicates that datablock has a category element diffrn_refln.
Abstract Datatype property for diffrn_refln items.