Refining the macromolecular model–achieving the best agreement with the data from X-ray diffraction experiment

Ivan G. Shabalin, Przemyslaw J. Porebski, Wladek Minor

Research output: Contribution to journalReview articlepeer-review

29 Scopus citations

Abstract

Refinement of macromolecular X-ray crystal structures involves using complex software with hundreds of different settings. The complexity of underlying concepts and the sheer amount of instructions may make it difficult for less experienced crystallographers to achieve optimal results in their refinements. This tutorial review offers guidelines for choosing the best settings for the reciprocal-space refinement of macromolecular models and provides practical tips for manual model correction. To help aspiring crystallographers navigate the process, some of the most practically important concepts of protein structure refinement are described. Among the topics covered are the use and purpose of R-free, geometrical restraints, restraints on atomic displacement parameters (ADPs), refinement weights, various parametrizations of ADPs (full anisotropic refinement and TLS), and omit maps. We also give practical tips for manual model correction in Coot, modelling of side-chains with poor or missing density, and ligand identification, fitting, and refinement.

Original languageEnglish
Pages (from-to)236-262
Number of pages27
JournalCrystallography Reviews
Volume24
Issue number4
DOIs
StatePublished - 2 Oct 2018
Externally publishedYes

Keywords

  • Structural biology
  • X-ray crystallography
  • ligands
  • protein crystal structure
  • refinement
  • reproducibility

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