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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. 18.4, p. 401
Section 18.4.6. Quality assessment of the model
a
National Cancer Institute, Brookhaven National Laboratory, Building 725A-X9, Upton, NY 11973, USA,bStructural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England, and CLRC, Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, England, and cStructural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England |
The refinement of proteins at resolution lower than atomic depends upon the use of restraints on the geometry and ADPs. Most target libraries for refinement and validation of structures (e.g. Engh & Huber, 1991![[link]](/graphics/greenarr.gif)
) are derived from either the Cambridge Structural Database (Allen et al., 1979) or from protein structures in the Protein Data Bank (PDB; Bernstein et al., 1977). The availability of atomic resolution structures provides more objective data for the construction of target libraries. Stereochemical parameters, such as conformational angles φ, ψ, should ideally not be restrained, as they allow independent validation of the model. Analysis of eight structures determined at atomic resolution (EU 3-D Validation Network, 1998) indicates that they follow the expected rules of chemistry more closely than those of lower-resolution analyses in the PDB, confirming that atomic resolution indeed provides more precise coordinates.
References
EU 3-D Validation Network (1998). Who checks the checkers? Four validation tools applied to eight atomic resolution structures. J. Mol. Biol. 276, 417–436.Google Scholar
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Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. E., Brice, M. D., Rogers, J. K., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977). The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535–542. Google Scholar
Engh, R. A. & Huber, R. (1991). Accurate bond and angle parameters for X-ray protein structure refinement. Acta Cryst. A47, 392–400.Google Scholar
