122d
From Proteopedia
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DNA HELIX STRUCTURE AND REFINEMENT ALGORITHM: COMPARISON OF MODELS FOR D(CCAGGCM==5==CTGG) DERIVED FROM NUCLSQ, TNT, AND X-PLOR
Overview
In an earlier study [Heinemann & Hahn (1992). J. Biol. Chem. 267, 7332-7341], the crystal structure of the double-stranded B-DNA decamer, d(CCAGGCm(5)CTGG) was refined with NUCLSQ to R = 17.4% against 3799 2sigma, structure amplitudes in the resolution range 8-1.7 A. This structure has, now been re-refined against the same diffraction data using either TNT or, X-PLOR in order to determine to what extent the resulting DNA, conformations would differ and to examine the suitability of these, programs for the refinement of oligonucleotide structures. The R value, from the NUCLSQ refinement could not be reached with either TNT or X-PLOR, although both programs yield reasonably refined DNA models showing, root-mean-square deviations against the NUCLSQ model of the decamer duplex, of 0.25 and 0.32 A, respectively. Some derived local structure parameters, differ depending on the refinement procedure used. This holds true for, several exocyclic torsion angles of the sugar-phosphate backbone, whereas, sugar puckers as well as helical and base-pair stacking parameters are, only weakly influenced. A subset of 15 solvent sites with low temperature, factors is conserved in all three models.
About this Structure
122D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
DNA helix structure and refinement algorithm: comparison of models for d(CCAGGCm5CTGG) derived from NUCLSQ, TNT and X-PLOR., Hahn M, Heinemann U, Acta Crystallogr D Biol Crystallogr. 1993 Sep 1;49(Pt 5):468-77. PMID:15299506
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