title: A new default restraint library for the protein backbone in Phenix: a conformation-dependent geometry goes mainstream.
abstract: 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 [Moriarty et 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 by Phenix is 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.affiliation: Physical Biosciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Nigel W
authors.initials: NW
authors.lastname: Moriarty
authors.affiliation: Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97377, USA.
authors.forename: Dale E
authors.initials: DE
authors.lastname: Tronrud
authors.affiliation: Physical Biosciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Paul D
authors.initials: PD
authors.lastname: Adams
authors.affiliation: Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97377, USA.
authors.forename: P Andrew
authors.initials: PA
authors.lastname: Karplus
mesh_terms: D018360:Crystallography, X-Ray; D030562:Databases, Protein; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D011506:Proteins
keywords: Phenix; covalent geometry restraints; crystallographic refinement; protein structure; validation