Display Settings:


Send to:

Choose Destination
See comment in PubMed Commons below
Acta Crystallogr D Biol Crystallogr. 2010 Jul;66(Pt 7):834-42. doi: 10.1107/S0907444910019207. Epub 2010 Jun 19.

Using a conformation-dependent stereochemical library improves crystallographic refinement of proteins.

Author information

  • 1Department of Biophysics and Biochemistry, Oregon State University, Corvallis, Oregon 97331, USA.


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.

[PubMed - indexed for MEDLINE]
Free PMC Article

Images from this publication.See all images (5)Free text

Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
PubMed Commons home

PubMed Commons

How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for International Union of Crystallography Icon for PubMed Central
    Loading ...
    Write to the Help Desk