242d: Difference between revisions

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==MAD PHASING STRATEGIES EXPLORED WITH A BROMINATED OLIGONUCLEOTIDE CRYSTAL AT 1.65 A RESOLUTION.==
==MAD PHASING STRATEGIES EXPLORED WITH A BROMINATED OLIGONUCLEOTIDE CRYSTAL AT 1.65 A RESOLUTION.==
<StructureSection load='242d' size='340' side='right' caption='[[242d]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
<StructureSection load='242d' size='340' side='right'caption='[[242d]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[242d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=242D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=242D FirstGlance]. <br>
<table><tr><td colspan='2'>[[242d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=242D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=242D FirstGlance]. <br>
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CBR:5-BROMO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>CBR</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.65&#8491;</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=242d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=242d OCA], [http://pdbe.org/242d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=242d RCSB], [http://www.ebi.ac.uk/pdbsum/242d PDBsum]</span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CBR:5-BROMO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>CBR</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=242d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=242d OCA], [https://pdbe.org/242d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=242d RCSB], [https://www.ebi.ac.uk/pdbsum/242d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=242d ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The crystal structure of a brominated oligonucleotide d(CGCG(Br)CG), chemical formula C(114)N(48)O(68)P(10)Br(2), has been analysed by multiwavelength anomalous dispersion (MAD) methods. The oligonucleotide crystallizes in space group P2(1)2(1)2(1) with a = 17.97, b = 30.98, c = 44.85 A, alpha = beta = gamma 90 degrees . Data to a resolution of 1.65 A were collected at four wavelengths about the K-absorption edge of the bromine atom (lambda(1) = 0.9323 A, a reference wavelength at the long-wavelength side of the edge; lambda(2) = 0.9192 A, at the absorption-edge inflection point; lambda(3) = 0.9185 A, at the ;white line' absorption maximum; lambda(4) = 0.8983 A, a reference wavelength at the short-wavelength side) using synchrotron radiation at Station PX9.5, SRS, Daresbury. Multiwavelength data could be collected on a single-crystal as the sample was radiation stable. Anomalous and dispersive Patterson maps were readily interpretable to give the bromine anomalous scatterer positions. Phase calculations to 1.65 A, resolution, using all four wavelengths, gave a figure of merit of 0.825 for 2454 reflections. The electron-density map was readily interpretable showing excellent connectivity for the sugar/phosphate backbone and each base was easily characterized. The two nucleotide strands paired up as expected in an antiparallel Watson-Crick-type manner. The structure was refined to 1.65 A using all the data (R-factor = 17.0% based on 3151 reflections, with a data-to-parameter ratio of 2.6). In addition to the four-wavelength analysis, a variety of other phasing strategies, and the associated quality of the resulting electron-density maps, were compared. These included use of either of the reference wavelength data sets in the two possible three-wavelength phasing combinations to assess their relative effectiveness. Moreover, the time dependence upon measuring the Bijvoet differences and its effect upon phasing was also investigated. Finally, the use of only two wavelengths, including Friedel pairs, is demonstrated (the theoretical minimum case); this is of particular interest when considering overall beam time needs and is clearly a feasible experimental strategy, as shown here.
MAD Phasing Strategies Explored with a Brominated Oligonucleotide Crystal at 1.65A Resolution.,Peterson MR, Harrop SJ, McSweeney SM, Leonard GA, Thompson AW, Hunter WN, Helliwell JR J Synchrotron Radiat. 1996 Jan 1;3(Pt 1):24-34. PMID:16702655<ref>PMID:16702655</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 242d" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Harrop, S J]]
[[Category: Large Structures]]
[[Category: Helliwell, J R]]
[[Category: Harrop SJ]]
[[Category: Hunter, W N]]
[[Category: Helliwell JR]]
[[Category: Leonard, G A]]
[[Category: Hunter WN]]
[[Category: McSweeney, S M]]
[[Category: Leonard GA]]
[[Category: Peterson, M R]]
[[Category: McSweeney SM]]
[[Category: Thompson, A W]]
[[Category: Peterson MR]]
[[Category: Dna]]
[[Category: Thompson AW]]
[[Category: Double helix]]
[[Category: Modified]]
[[Category: Z-dna]]

Latest revision as of 12:09, 14 February 2024

MAD PHASING STRATEGIES EXPLORED WITH A BROMINATED OLIGONUCLEOTIDE CRYSTAL AT 1.65 A RESOLUTION.MAD PHASING STRATEGIES EXPLORED WITH A BROMINATED OLIGONUCLEOTIDE CRYSTAL AT 1.65 A RESOLUTION.

Structural highlights

242d is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.65Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

242d, resolution 1.65Å

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