Journal
CRYSTALLOGRAPHY REVIEWS
Volume 24, Issue 4, Pages 236-262Publisher
TAYLOR & FRANCIS LTD
DOI: 10.1080/0889311X.2018.1521805
Keywords
Structural biology; X-ray crystallography; protein crystal structure; refinement; ligands; reproducibility
Categories
Funding
- National Institute of General Medical Sciences [GM117080, GM117325]
- National Institutes of Health BD2K program [HG008424]
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services [HHSN272201700060C, HHSN272201200026C]
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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.
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