A new default restraint library for the protein backbone in Phenix: a conformation-dependent geometry goes mainstream
Chemical restraints are a fundamental part of crystallographic protein structure refinement. In response to mounting evidence that conventional restraints have shortcomings, it has previously been documented that using backbone restraints that depend on the protein backbone conformation helps to address these shortcomings and improves the performance of refinements [Moriartyet al.(2014),FEBS J.281, 4061–4071]. It is important that these improvements be made available to all in the protein crystallography community. Toward this end, a change in the default geometry library used byPhenixis described here. Tests are presented showing that this change will not generate increased numbers of outliers during validation, or deposition in the Protein Data Bank, during the transition period in which some validation tools still use the conventional restraint libraries.
- Authors:
-
[1]
; [2]
; [3]
; [2]
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Biosciences
- Oregon State Univ., Corvallis, OR (United States). Dept. of Biochemistry and Biophysics
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Biosciences; Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering
- Publication Date:
- Grant/Contract Number:
- AC02-05CH11231; R01-GM083136; 1P01 GM063210
- Type:
- Accepted Manuscript
- Journal Name:
- Acta Crystallographica. Section D. Structural Biology
- Additional Journal Information:
- Journal Volume: 72; Journal Issue: 1; Journal ID: ISSN 2059-7983
- Publisher:
- IUCr
- Research Org:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Org:
- USDOE; National Institutes of Health (NIH)
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; covalent geometry restraints; crystallographic refinement; protein structure; validation; Phenix
- OSTI Identifier:
- 1378757
- Free Publicly Accessible Full Text
-
Accepted Manuscript (DOE)
- Publisher's Version of Record
- https://doi.org/10.1107/S2059798315022408