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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== |
| The line below this paragraph, containing "STRUCTURE_123d", creates the "Structure Box" on the page.
| | <StructureSection load='123d' size='340' side='right'caption='[[123d]], [[Resolution|resolution]] 1.70Å' scene=''> |
| You may change the PDB parameter (which sets the PDB file loaded into the applet)
| | == Structural highlights == |
| or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| | <table><tr><td colspan='2'>[[123d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=123D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=123D FirstGlance]. <br> |
| or leave the SCENE parameter empty for the default display.
| | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7Å</td></tr> |
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| | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene></td></tr> |
| {{STRUCTURE_123d| PDB=123d | SCENE= }}
| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=123d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=123d OCA], [https://pdbe.org/123d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=123d RCSB], [https://www.ebi.ac.uk/pdbsum/123d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=123d ProSAT]</span></td></tr> |
| | | </table> |
| '''DNA HELIX STRUCTURE AND REFINEMENT ALGORITHM: COMPARISON OF MODELS FOR D(CCAGGCM==5==CTGG) DERIVED FROM NUCLSQ, TNT, AND X-PLOR'''
| | __TOC__ |
| | | </StructureSection> |
| | | [[Category: Large Structures]] |
| ==Overview== | | [[Category: Hahn M]] |
| 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.
| | [[Category: Heinemann U]] |
| | |
| ==About this Structure== | |
| 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]
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| [[Category: Hahn, M.]] | |
| [[Category: Heinemann, U.]] | |
| [[Category: B-dna]] | |
| [[Category: Double helix]] | |
| [[Category: Modified]] | |
| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 09:27:43 2008''
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