title: Using a conformation-dependent stereochemical library improves crystallographic refinement of proteins.
abstract: The major macromolecular crystallographic refinement packages restrain models to ideal geometry targets defined as single values that are independent of molecular conformation. However, ultrahigh-resolution X-ray models of proteins are not consistent with this concept of ideality and have been used to develop a library of ideal main-chain bond lengths and angles that are parameterized by the phi/psi angle of the residue [Berkholz et al. (2009), Structure, 17, 1316-1325]. Here, it is first shown that the new conformation-dependent library does not suffer from poor agreement with ultrahigh-resolution structures, whereas current libraries have this problem. Using the TNT refinement package, it is then shown that protein structure refinement using this conformation-dependent library results in models that have much better agreement with library values of bond angles with little change in the R values. These tests support the value of revising refinement software to account for this new paradigm.
authors.affiliation: Department of Biophysics and Biochemistry, Oregon State University, Corvallis, Oregon 97331, USA.
authors.forename: Dale E
authors.initials: DE
authors.lastname: Tronrud
authors.forename: Donald S
authors.initials: DS
authors.lastname: Berkholz
authors.forename: P Andrew
authors.initials: PA
authors.lastname: Karplus
mesh_terms: D018360:Crystallography, X-Ray / Q000379:methods*; D030562:Databases, Protein; D011487:Protein Conformation; D011506:Proteins / Q000032:analysis* / Q000737:chemistry
chemical_list: D011506:Proteins