Using a conformation-dependent stereochemical library improves crystallographic refinement of proteins
A stereochemical library which defines the target values for main-chain bond lengths and angles as a function of the residue’s ϕ/ψ angles was tested in refinement. Use of this library allows the construction of models that conform to ideal geometry much better than previous libraries without degrading their fit to the diffraction data. 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 ϕ/ψ 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.
- OSTI ID:
- 22351210
- Journal Information:
- Acta Crystallographica. Section D: Biological Crystallography, Vol. 66, Issue Pt 7; Other Information: PMCID: PMC2897700; PMID: 20606264; PUBLISHER-ID: dz5202; OAI: oai:pubmedcentral.nih.gov:2897700; Copyright (c) International Union of Crystallography 2010; Country of input: International Atomic Energy Agency (IAEA); ISSN 0907-4449
- Country of Publication:
- Denmark
- Language:
- English
Similar Records
A conformation-dependent stereochemical library improves crystallographic refinement even at atomic resolution
Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement