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. 160-161

Section 3.6.6.2.3. Restraints and refinement by shells of resolution

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

3.6.6.2.3. Restraints and refinement by shells of resolution

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The data items in these categories are as follows:

(a) REFINE_LS_RESTR [Scheme scheme64]

(b) REFINE_LS_RESTR_NCS [Scheme scheme66]

(c) REFINE_LS_RESTR_TYPE [Scheme scheme67]

(d) REFINE_LS_SHELL [Scheme scheme68]

(e) REFINE_LS_CLASS [Scheme scheme69]

The bullet ([\bullet]) indicates a category key. Where multiple items within a category are marked with a bullet, they must be taken together to form a compound key. The arrow ([\rightarrow]) is a reference to a parent data item.

These categories were introduced in the mmCIF dictionary to allow a detailed description of several aspects of structure refinement to be given. Data items in the REFINE_LS_RESTR category allow geometric restraints to be specified and the deviations of restrained parameters from ideal values in the final model to be given. The type of the geometric restraints can be described in more detail using data items in the REFINE_LS_RESTR_TYPE category. Data items in the REFINE_LS_RESTR_NCS category can be used to give information about any restraints on noncrystallographic symmetry used in the refinement and the category REFINE_LS_SHELL contains data items that allow the results of refinement to be given by shells of resolution.

Data items in the REFINE_LS_RESTR category can be used to record details about the restraints applied to various classes of parameters during least-squares refinement (Example 3.6.6.9[link]). It is clearly useful to tabulate the various classes of restraint, their deviation from ideal target values and the criteria used to reject parameters that lie too far from a target, as these data are often published as part of a description of the refinement and are often deposited with the coordinates in an archive. However, the types of restraints applied depend strongly on the software package used, and as new refinement packages regularly become available, it was clearly not advisable to provide program-specific data items in the mmCIF dictionary. The approach taken in the mmCIF dictionary has been to allow the value of _refine_ls_restr.type to be a free-text field, so that arbitrary labels can be given to restraints that are particular to a software package, but to recommend the use of specific labels for restraints applied by particular programs. The dictionary provides examples for labels specific to the programs PROTIN/PROLSQ (Hendrickson & Konnert, 1979[link]) and RESTRAIN (Driessen et al., 1989[link]). These program-specific representations have particular prefixes; thus the value p_bond_d is a bond-distance restraint as applied by PROTIN/PROLSQ. Values for _refine_ls_restr.type appropriate for other refinement programs may be suggested in future versions of the mmCIF dictionary.

Example 3.6.6.9. Results of the refinement of an HIV-1 protease structure (PDB 5HVP) described with data items in the REFINE_LS_RESTR and REFINE_LS_SHELL categories.

[Scheme scheme70]

Data items in the REFINE_LS_RESTR_TYPE category can be used to specify the ranges within which quantities are allowed to vary for each type of restraint. The special value indicated by a full stop (.) represents a restraint unbounded on the high or low side.

Data items in the REFINE_LS_RESTR_NCS category can be used to record details about the restraints applied to atom positions in domains related by noncrystallographic symmetry during least-squares refinement, and also to record the deviation of the restrained atomic parameters at the end of the refinement. The domains related by noncrystallographic symmetry are defined in the STRUCT_NCS_DOM and related categories (see Section 3.6.7.5.5[link]). The quantities that can be recorded for each restrained domain are the root-mean-square deviations of the displacement and positional parameters, and the weighting coefficients used in the noncrystallographic restraint of each type of parameter. Any special aspects of the way the restraints were applied may be described using _refine_ls_restr_ncs.ncs_model_details.

Data items in the REFINE_LS_SHELL category are used to summarize details of the results of the least-squares refinement by shells of resolution (Example 3.6.6.9[link]). The resolution range, in ångströms, forms the category key; for each shell the quantities reported, such as the number of reflections above the threshold for counting as significantly intense, are all defined in the same way as the corresponding data items used to describe the results of the overall refinement in the REFINE category.

The core dictionary category REFINE_LS_CLASS was introduced after the release of the first version of the mmCIF dictionary. It provides a more general way of describing the treatment of particular subsets of the observations, but it is not expected to be used in macromolecular structural studies, where partition by shells of resolution is traditional.

References

Driessen, H., Haneef, M. I. J., Harris, G. W., Howlin, B., Khan, G. & Moss, D. S. (1989). RESTRAIN: restrained structure-factor least-squares refinement program for macromolecular structures. J. Appl. Cryst. 22, 510–516.
Hendrickson, W. A. & Konnert, J. H. (1979). Stereochemically restrained crystallographic least-squares refinement of macromolecule structures. In Biomolecular structure, conformation, function and evolution, edited by R. Srinavisan, Vol. I, pp. 43–57. New York: Pergamon Press.








































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