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Crystal Structure RefinementA Crystallographer's Guide to SHELXL$
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Peter Müller, Regine Herbst-Irmer, Anthony L. Spek, Thomas R. Schneider, and Michael R. Sawaya

Print publication date: 2006

Print ISBN-13: 9780198570769

Published to Oxford Scholarship Online: September 2010

DOI: 10.1093/acprof:oso/9780198570769.001.0001

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Protein structure (cross) validation

Protein structure (cross) validation

Chapter:
(p.187) 11 Protein structure (cross) validation
Source:
Crystal Structure Refinement
Author(s):

Michael R. Sawaya

Publisher:
Oxford University Press
DOI:10.1093/acprof:oso/9780198570769.003.0011

Cross validation is a key concept in attaining accuracy in crystallographic refinement. Refinement of protein structures is especially subject to model bias; an unchecked imagination during the model building process or an inattentiveness to detail can reinforce features in the electron density map that are incorrect. The problem of model bias stems from the fact that protein structure refinement is almost always an underdetermined problem, as a medium-resolution dataset does not contain a sufficient number of structure factors to justify the number of parameters refined. Besides explaining the concept of Rfree, this chapter describes the algorithms of the programs PROCHECK, WHATCHECK, Verify3D, ERRAT, and PROVE. Program outputs are illustrated and interpreted for a particular example.

Keywords:   Rfree, PROCHECK, WHATCHECK, Verify3D, ERRAT, PROVE

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