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International
Tables for Crystallography Volume F Crystallography of biological macromolecules Edited by M. G. Rossmann and E. Arnold © International Union of Crystallography 2006 |
International Tables for Crystallography (2006). Vol. F. ch. 24.5, pp. 676-677
Section 24.5.2.2. Validation
H. M. Berman,a* J. Westbrook,a Z. Feng,a G. Gilliland,b T. N. Bhat,b H. Weissig,c I. N. Shindyalovc and P. E. Bourned
a
Department of Chemistry, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854-8087, USA,bNational Institute of Standards and Technology, Biotechnology Division, 100 Bureau Drive, Gaithersburg, MD 20899, USA,cSan Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0537, USA, and dDepartment of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0537, USA |
Validation refers to the procedure for assessing the quality of deposited atomic models (structure validation) and for assessing how well these models fit the experimental data (experimental validation). The PDB validates structures using accepted community standards as part of ADIT's integrated data-processing system. All validation reports are communicated directly to the depositor. It is also possible to run these validation checks against structures that are not being deposited. A validation server (http://deposit.rcsb.org/validate/ ) has been made available for this purpose.
Several types of checks are used in this process: PROCHECK (Laskowski et al., 1993![[link]](/graphics/greenarr.gif)
) is used for checking the structural features of proteins and NUCheck (Feng, Westbrook & Berman, 1998) is used for checking the structural features of nucleic acids. The information currently checked includes the following: bond lengths and bond angles, nomenclature, sequence, stereochemistry, torsion angles, ligand geometry, planarity of peptide bonds, intermolecular contacts, and positions of water molecules. In consultation with the community, other structure checks will be implemented over the next few years.
The experimental data are also checked. Currently, X-ray crystallographic data are validated and plans for checking NMR data are in progress. For X-ray crystallographic structures, the structure factors are validated using SFCHECK (Vaguine et al., 1999). This program extracts the deposited R factor, resolution and model information, and then compares them with values calculated from coordinate and structure-factor files. It also calculates an overall B factor, coordinate errors, an effective resolution and completeness. The summary of the density correlation shift and B factor are reported for each residue. As specific procedures are developed for checking NMR structures against experimental data, they will be incorporated into the PDB validation procedures.
References
Feng, Z., Westbrook, J. & Berman, H. M. (1998). NUCheck. NDB-407. Rutgers University, New Brunswick, NJ, USA.Google Scholar
Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M. (1993). PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26, 283–291.Google Scholar
Vaguine, A. A., Richelle, J. & Wodak, S. J. (1999). SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. Acta Cryst. D55, 191–205.Google Scholar
