New parameters for the refinement of nucleic acid-containing structures

Gary Parkinson, Jaroslav Vojtechovaky, Lester Clowney, Axel T. Brünger, Helen M. Berman

Research output: Contribution to journalArticlepeer-review

254 Scopus citations

Abstract

Structures at atomic resolution (up to 1.0 Å) which contain bases, sugars or the phosphodiester linkage, were selected from the Nucleic Acid Database or the Cambridge Structural Database to build a nucleic acid dictionary from X-ray refined structures. The dictionary consists of the average values for bond distances, bond angles and dihedral angles. The variance of the sample is used to provide information about the expected r.m.s. deviations of the refined parameters. A dictionary was constructed for refinement trials in X-PLOR. The dictionary includes RNA and DNA in C2′-endo and C3′-endo sugar pucker conformations, as well as values for the backbone dihedrals. Tests were performed on the dictionary using three structures: a B-DNA, a Z-DNA and a protein-DNA complex. During the course of refinement, all three structures showed significant improvements as measured by r.m.s. deviations and R factors when compared to the previous DNA dictionary.

Original languageEnglish (US)
Pages (from-to)57-64
Number of pages8
JournalActa Crystallographica Section D: Biological Crystallography
Volume52
Issue number1
DOIs
StatePublished - Jan 1 1996

All Science Journal Classification (ASJC) codes

  • Structural Biology

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