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Open data
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Basic information
Entry | Database: PDB / ID: 4re7 | ||||||||||||||||||||
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Title | Lambda-[Ru(TAP)2(dppz)]2+ bound to d(TCIGCGCCGA) | ||||||||||||||||||||
![]() | 5'-D(*![]() DNA / inosine / kinking / ruthenium | Function / homology | : / Ru(tap)2(dppz) complex / DNA | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() Hall, J.P. / Cardin, C.J. | ![]() ![]() Title: The effects of DNA modification on the binding of polypyridyl ruthenium complexes Authors: Hall, J.P. / Gurung, S.P. / Beer, H. / Buchner, K. / 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 | ![]() | 23.5 KB | Display | ![]() |
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PDB format | ![]() | 14.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 718.1 KB | Display | ![]() |
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Full document | ![]() | 718.8 KB | Display | |
Data in XML | ![]() | 2.6 KB | Display | |
Data in CIF | ![]() | 2.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 3.03 Å3/Da / Density % sol: 59.4 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1 uL 2 mM oligonucleotide (double HPLC-purified) + 1 uL 2 mM lambda-[Ru(TAP)2(dppz)]Cl2 + 6 uL 10% v/v MPD, 40 mM sodium cacodylate, pH 6.0, 12 mM spermine tetrahydrochloride, 80 mM sodium ...Details: 1 uL 2 mM oligonucleotide (double HPLC-purified) + 1 uL 2 mM lambda-[Ru(TAP)2(dppz)]Cl2 + 6 uL 10% v/v MPD, 40 mM sodium cacodylate, pH 6.0, 12 mM spermine tetrahydrochloride, 80 mM sodium chloride, 20 mM barium chloride equilibrated against 1 mL 35% v/v MPD, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2014 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→47.83 Å / Num. all: 2012 / Num. obs: 2012 / % possible obs: 94.1 % / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.18→2.24 Å / Redundancy: 10.7 % / Rmerge(I) obs: 1.122 / Mean I/σ(I) obs: 1.9 / % possible all: 93 |
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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: 2.181→33.821 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.181→33.825 Å
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Refinement TLS params. | Method: refined / Origin x: 10.5399 Å / Origin y: 11.9227 Å / Origin z: -19.6956 Å
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Refinement TLS group | Selection details: chain 'A' |