+Open data
-Basic information
Entry | Database: PDB / ID: 2o1i | ||||||||||||||||||
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Title | RH(BPY)2CHRYSI complexed to mismatched DNA | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / DNA mismatch / metallointercalator / DNA recognition | Function / homology | Chem-R1C / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.1 Å | Authors | Pierre, V.C. / Kaiser, J.T. / Barton, J.K. | Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007 | Title: Insights into finding a mismatch through the structure of a mispaired DNA bound by a rhodium intercalator. Authors: Pierre, V.C. / Kaiser, J.T. / Barton, J.K. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2o1i.cif.gz | 34 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o1i.ent.gz | 24 KB | Display | PDB format |
PDBx/mmJSON format | 2o1i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o1/2o1i ftp://data.pdbj.org/pub/pdb/validation_reports/o1/2o1i | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-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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Details | The second part of the biological assembly is generated by the two fold axis y,x,-z. |
-Components
#1: DNA chain | Mass: 3647.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: solid phase synthesis | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 56.63 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: SrCl2 40mM, MgCl2 10mM, Na-cacodylate 20mM, spermine-4HCl 6mM, MPD 5%(v/v)equilibrated against 35% MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.1→24 Å / Num. obs: 17269 / % possible obs: 94 % / Redundancy: 8.7 % / Biso Wilson estimate: 14.85 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Net I/σ(I): 13.4 | ||||||||||||||||||
Reflection shell | Resolution: 1.07→1.14 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.015 / Mean I/σ(I) obs: 0.9 / Rsym value: 1.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO / Highest resolution: 1.1 Å / Num. parameters: 4070 / Num. restraintsaints: 5578 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 2 / Occupancy sum hydrogen: 178 / Occupancy sum non hydrogen: 384 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.1 Å
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Refine LS restraints |
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