123d: Difference between revisions

Revision as of 09:27, 2 May 2008

DNA HELIX STRUCTURE AND REFINEMENT ALGORITHM: COMPARISON OF MODELS FOR D(CCAGGCM==5==CTGG) DERIVED FROM NUCLSQ, TNT, AND X-PLOR

OverviewOverview

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 StructureAbout this Structure

Full crystallographic information is available from OCA.

ReferenceReference

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 Page seeded by OCA on Fri May 2 09:27:43 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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 [[Image:123d.gif|left|200px]]
- {{Structure
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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'''
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 ==About this Structure==
-D is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=123D OCA].
+Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=123D 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:[http://www.ncbi.nlm.nih.gov/pubmed/15299506 15299506]
-[[Category: Protein complex]]
 [[Category: Hahn, M.]]
 [[Category: Heinemann, U.]]
-[[Category: b-dna]]
+[[Category: B-dna]]
-[[Category: double helix]]
+[[Category: Double helix]]
-[[Category: modified]]
+[[Category: Modified]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 09:27:43 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:27:13 2008''