Acta Cryst D - Structural Biology
Volume 72| Part 1| January 2016| Pages 176-179
A new default restraint library for the protein backbone in Phenix: a conformation-dependent geometry goes mainstream
aPhysical Biosciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, bDepartment of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97377, USA, and cDepartment of Bioengineering, University of California Berkeley, Berkeley, CA 94720, USA
Edited by R. J. Read, University of Cambridge, England (Received 5 October 2015; accepted 23 November 2015)
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.
Keywords: covalent geometry restraints; crystallographic refinement; protein structure; validation; Phenix.