Anomalies in the refinement of isoleucine
- Radboud University Medical Center, Geert Grooteplein 26-28, 6525 GA Nijmegen (Netherlands)
The side-chain torsion angles of isoleucines in X-ray protein structures are a function of resolution, secondary structure and refinement software. Detailing the standard torsion angles used in refinement software can improve protein structure refinement. A study of isoleucines in protein structures solved using X-ray crystallography revealed a series of systematic trends for the two side-chain torsion angles χ{sub 1} and χ{sub 2} dependent on the resolution, secondary structure and refinement software used. The average torsion angles for the nine rotamers were similar in high-resolution structures solved using either the REFMAC, CNS or PHENIX software. However, at low resolution these programs often refine towards somewhat different χ{sub 1} and χ{sub 2} values. Small systematic differences can be observed between refinement software that uses molecular dynamics-type energy terms (for example CNS) and software that does not use these terms (for example REFMAC). Detailing the standard torsion angles used in refinement software can improve the refinement of protein structures. The target values in the molecular dynamics-type energy functions can also be improved.
- OSTI ID:
- 22347790
- Journal Information:
- Acta Crystallographica. Section D: Biological Crystallography, Vol. 70, Issue Pt 4; Other Information: PMCID: PMC3975889; PMID: 24699648; PUBLISHER-ID: kw5073; OAI: oai:pubmedcentral.nih.gov:3975889; Copyright (c) Berntsen & Vriend 2014; This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.; Country of input: International Atomic Energy Agency (IAEA); ISSN 0907-4449
- Country of Publication:
- Denmark
- Language:
- English
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