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Open data
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Basic information
Entry | Database: PDB / ID: 5iu5 | |||||||||||||||||||||||||||||||
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Title | Lambda-[Ru(TAP)2(dppz)]2+ bound to d(TCGGCICCGA)2 | |||||||||||||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / ruthenium / intercalation / photooxidising | Function / homology | : / Ru(tap)2(dppz) complex / DNA | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() Hall, J.P. / Cardin, C.J. | Funding support | | ![]()
![]() ![]() Title: Unexpected enhancement of sensitised photo-oxidation by a Ru(II) complex on replacement of guanine with inosine in DNA Authors: Keane, P.M. / Hall, J.P. / Poynton, F.E. / Gurung, S.P. / Clark, I.P. / Sazanovich, I.V. / Towrie, M. / Gunnlaugsson, T. / Brazier, J.A. / Quinn, S.J. / Cardin, C.J. / Kelly, J.M. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 25 KB | Display | ![]() |
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PDB format | ![]() | 14.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 765.7 KB | Display | ![]() |
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Full document | ![]() | 765 KB | Display | |
Data in XML | ![]() | 2.7 KB | Display | |
Data in CIF | ![]() | 3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar 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
#1: DNA chain | Mass: 3030.979 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: Chemical | ChemComp-BA / |
#3: Chemical | ChemComp-RKL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.58 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 1uL 2mM d(TCGGCICCGA) 1uL 4mM rac-RuTAP2dppz 6uL of a solution containing 20mM BaCl2, 80mM KCl, 40mM Na-cacodylate pH 7, 12mM spermine, 10% (V/V) hexylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 16, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→47.78 Å / Num. obs: 3067 / % possible obs: 93.9 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.034 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.985 / Mean I/σ(I) obs: 1.6 / % possible all: 93.1 |
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Processing
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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 / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→33.786 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 13.244 Å / Origin y: 11.9997 Å / Origin z: -3.5719 Å
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Refinement TLS group | Selection details: chain c |