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- PDB-5jev: del-[Ru(phen)2(dppz]2+ bound to d(TCGGCGCCGA) with Cobalt hexammine -
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Open data
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Basic information
Entry | Database: PDB / ID: 5jev | ||||||||||||||||||||
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Title | del-[Ru(phen)2(dppz]2+ bound to d(TCGGCGCCGA) with Cobalt hexammine | ||||||||||||||||||||
![]() | DNA (5'-D(*![]() ![]() ![]() ![]() Function / homology | Delta-Ru(phen)2(dppz) complex / COBALT HEXAMMINE(III) / | ![]() ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() Hall, J.P. / Cardin, C.J. | ![]() ![]() Title: Delta chirality ruthenium 'light-switch' complexes can bind in the minor groove of DNA with five different binding modes. Authors: Hall, J.P. / Keane, P.M. / Beer, H. / Buchner, K. / Winter, G. / Sorensen, T.L. / Cardin, D.J. / Brazier, J.A. / Cardin, C.J. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 41.7 KB | Display | ![]() |
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PDB format | ![]() | 30.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: DNA chain | Mass: 3045.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||
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#2: Chemical | #3: Chemical | ChemComp-NCO / | #4: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.85 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 1uL 2mM d(TCGGCGCCGA), 1uL 2mM del-[Ru(phen)2(dppz)]2+, 6uL of a solution containing 10% (V/V) 2-methyl-2,4-pentanediol, 40mM Na-cacodylate, 20mM Cobalt hexammine, 12mM NaCl and 80mM KCl. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 14, 2012 |
Radiation | Monochromator: dual Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 0.99→22.61 Å / Num. obs: 19226 / % possible obs: 94.1 % / Observed criterion σ(F): -3 / Redundancy: 6.5 % / CC1/2: 1 / Rmerge(I) obs: 0.031 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 0.99→1.02 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.833 / Mean I/σ(I) obs: 1.9 / % possible all: 92.2 |
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Processing
Software |
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.99→18.901 Å
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Refine LS restraints |
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LS refinement shell |
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