International
Tables for
Crystallography
Volume G
Definition and exchange of crystallographic data
Edited by S. R. Hall and B. McMahon

International Tables for Crystallography (2006). Vol. G, ch. 3.6, pp. 161-162

Section 3.6.6.2.4. Equivalent atoms in the refinement

P. M. D. Fitzgerald,a* J. D. Westbrook,b P. E. Bourne,c B. McMahon,d K. D. Watenpaughe and H. M. Bermanf

aMerck Research Laboratories, Rahway, New Jersey, USA,bProtein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, New Jersey, USA,cResearch Collaboratory for Structural Bioinformatics, San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0537, USA,dInternational Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England,eretired; formerly Structural, Analytical and Medicinal Chemistry, Pharmacia Corporation, Kalamazoo, Michigan, USA, and fProtein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, New Jersey, USA
Correspondence e-mail:  paula_fitzgerald@merck.com

3.6.6.2.4. Equivalent atoms in the refinement

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The data items in these categories are as follows:

(a) REFINE_B_ISO [Scheme scheme71]

(b) REFINE_OCCUPANCY [Scheme scheme72]

The bullet ([\bullet]) indicates a category key.

In macromolecular structure refinement, displacement factors or occupancies are often treated as equivalent for groups of atoms. An example would be the case where most of the atoms in the structure are refined with isotropic displacement factors, but a bound metal atom is allowed to refine anisotropically. Another example would be where the occupancies for all of the atoms in the protein part of a macromolecular complex are fixed at 1.0, but the occupancies of atoms in a bound inhibitor are refined. The REFINE_B_ISO and REFINE_OCCUPANCY categories can be used to record this information (Example 3.6.6.10[link]).

Example 3.6.6.10. The handling of displacement factors and occupancies during the refinement of an HIV-1 protease structure (PDB 5HVP) described with data items in the REFINE_B_ISO and REFINE_OCCUPANCY categories.

[Scheme scheme73]

Data items in the REFINE_B_ISO category can be used to record details of the treatment of isotropic B (displacement) factors during refinement. There is no formal link between the classes identified by _refine_B_iso.class and individual atom sites, although relationships may be inferred if the class names are carefully chosen. The category allows the treatment of the atoms in each class (isotropic, anisotropic or fixed) and the value assigned for fixed isotropic B factors to be recorded. Any special details can be given in a free-text field.

Data items in the REFINE_OCCUPANCY category can be used to record details of the treatment of occupancies of groups of atom sites during refinement. As with the treatment of displacement factors in the REFINE_B_ISO category, the classes itemized by _refine_occupancy.class are not formally linked to the individual atom sites, but the relationships may be deduced if the class names are chosen carefully.








































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