Chapter 21.1 Validation of protein crystal structures

Crystallography of biological macromolecules

First Online Edition (2006)

Part 21. Structure validation

  1. G. J. Kleywegt

Published Online: 1 JAN 2006

DOI: 10.1107/97809553602060000707

International Tables for Crystallography

International Tables for Crystallography

How to Cite

Kleywegt, G. J. 2006. Validation of protein crystal structures. International Tables for Crystallography. F:21:21.1:497–506.

Author Information

  1. Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE‐751 24 Uppsala, Sweden

Publication History

  1. Published Online: 1 JAN 2006



Since the process of building and refining a model of a biomacromolecule based on crystallographic data is subjective, quality‐control techniques are required to assess the validity of such models. During the 1990s, much experience was gained; the methods used and some of the lessons learned are reviewed here. In addition, an extensive compendium of quality criteria and quality‐control methods that are or have been used to validate models of biomacromolecules has been compiled. The emphasis in this compendium is on the validation of protein crystal structures.


  • accuracy;
  • atomic displacement parameters (temperature factors);
  • Calpha‐only model;
  • coordinate errors;
  • data completeness;
  • data resolution;
  • difference density quality;
  • errors;
  • merging R factors;
  • noncrystallographic symmetry;
  • outliers;
  • quality indicators;
  • real‐space fit;
  • signal strength and structure validation;
  • solvent;
  • structure validation;
  • temperature factors (atomic displacement parameters);
  • unit‐cell parameters