Chapter 21.1 Validation of protein crystal structures

Crystallography of biological macromolecules

Second Online Edition (2012)

Part 21. Structure validation

  1. G. J. Kleywegt

Published Online: 14 APR 2012

DOI: 10.1107/97809553602060000879

International Tables for Crystallography

International Tables for Crystallography

How to Cite

Kleywegt, G. J. 2012. Validation of protein crystal structures. International Tables for Crystallography. F:21:21.1:649–661.

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: 14 APR 2012


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