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Title: Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement

Ideal values of bond angles and lengths used as external restraints are crucial for the successful refinement of protein crystal structures at all but the highest of resolutions. The restraints in common usage today have been designed based on the assumption that each type of bond or angle has a single ideal value independent of context. However, recent work has shown that the ideal values are, in fact, sensitive to local conformation, and as a first step toward using such information to build more accurate models, ultra-high resolution protein crystal structures have been used to derive a conformation-dependent library (CDL) of restraints for the protein backbone (Berkholz et al. 2009. Structure. 17, 1316). Here, we report the introduction of this CDL into the Phenix package and the results of test refinements of thousands of structures across a wide range of resolutions. These tests show that use of the conformation dependent library yields models that have substantially better agreement with ideal main-chain bond angles and lengths and, on average, a slightly enhanced fit to the X-ray data. No disadvantages of using the backbone CDL are apparent. In Phenix usage of the CDL can be selected by simply specifying the cdl=True option.more » This successful implementation paves the way for further aspects of the context-dependence of ideal geometry to be characterized and applied to improve experimental and predictive modelling accuracy.« less
Authors:
 [1] ;  [2] ;  [3] ;  [2]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  2. Oregon State Univ., Corvallis, OR (United States). Dept. of Biochemistry and Biophysics
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering
Publication Date:
OSTI Identifier:
1172901
Grant/Contract Number:
AC02-05CH11231; R01-GM083136; 1P01-GM063210;
Type:
Accepted Manuscript
Journal Name:
Federation of European Biochemical Societies (FEBS) Journal
Additional Journal Information:
Journal Name: Federation of European Biochemical Societies (FEBS) Journal; Journal Volume: 281; Journal Issue: 18; Journal ID: ISSN 1742-464X
Publisher:
Federation of European Biochemical Societies
Research Org:
Univ. of California, Berkeley, CA (United States)
Sponsoring Org:
USDOE
Contributing Orgs:
Phenix Industrial Consortium
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 97 MATHEMATICS AND COMPUTING Protein structure; Crystallographic refinement; Geometry restraints; Ideal geometry; Structural genomics