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Title: 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]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Biosciences
  2. Oregon State Univ., Corvallis, OR (United States). Dept. of Biochemistry and Biophysics
  3. 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

Moriarty, Nigel W., Tronrud, Dale E., Adams, Paul D., and Karplus, P. Andrew. A new default restraint library for the protein backbone in Phenix: a conformation-dependent geometry goes mainstream. United States: N. p., Web. doi:10.1107/S2059798315022408.
Moriarty, Nigel W., Tronrud, Dale E., Adams, Paul D., & Karplus, P. Andrew. A new default restraint library for the protein backbone in Phenix: a conformation-dependent geometry goes mainstream. United States. doi:10.1107/S2059798315022408.
Moriarty, Nigel W., Tronrud, Dale E., Adams, Paul D., and Karplus, P. Andrew. 2016. "A new default restraint library for the protein backbone in Phenix: a conformation-dependent geometry goes mainstream". United States. doi:10.1107/S2059798315022408. https://www.osti.gov/servlets/purl/1378757.
@article{osti_1378757,
title = {A new default restraint library for the protein backbone in Phenix: a conformation-dependent geometry goes mainstream},
author = {Moriarty, Nigel W. and Tronrud, Dale E. and Adams, Paul D. and Karplus, P. Andrew},
abstractNote = {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.},
doi = {10.1107/S2059798315022408},
journal = {Acta Crystallographica. Section D. Structural Biology},
number = 1,
volume = 72,
place = {United States},
year = {2016},
month = {1}
}

Works referenced in this record:

A short history of SHELX
journal, December 2007
  • Sheldrick, George M.
  • Acta Crystallographica Section A Foundations of Crystallography, Vol. 64, Issue 1, p. 112-122
  • DOI: 10.1107/S0108767307043930

PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010
  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
  • DOI: 10.1107/S0907444909052925