+Open data
-Basic information
Entry | Database: PDB / ID: 4x1a | |||||||||||||||||||||||||||||||
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Title | Lambda-[Ru(TAP)2(dppz-10,12-Me)]2+ bound to d(TCGGCGCCGA) | |||||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / Ruthenium / polypyridyl | Function / homology | Chem-3WB / : / DNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 0.89 Å | Authors | Hall, J.P. / Cardin, C.J. | Funding support | United Kingdom, 1items |
Citation | Journal: Organometallics / Year: 2015 | Title: The Structural Effect of Methyl Substitution on the Binding of Polypyridyl Ru-dppz Complexes to DNA Authors: Hall, J.P. / Beer, H. / Buchner, K. / Cardin, D.J. / Cardin, C.J. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4x1a.cif.gz | 34.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x1a.ent.gz | 23.1 KB | Display | PDB format |
PDBx/mmJSON format | 4x1a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x1/4x1a ftp://data.pdbj.org/pub/pdb/validation_reports/x1/4x1a | HTTPS FTP |
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-Related structure data
-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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-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 | ChemComp-3WB / ( |
#3: Chemical | ChemComp-BA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.55 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1uL 2mM d(TCGGCGCCGA), 1ul 4mM rac-[Ru(TAP)2(dppz-10,12-Me)]2+, 6ul of a solution containing 20mM BaCl2, 80mM KCl, 12mM Spermine, 40mM Na-cacodylate pH 7, 10% v/v 2-methyl-2,4-pentanediol. ...Details: 1uL 2mM d(TCGGCGCCGA), 1ul 4mM rac-[Ru(TAP)2(dppz-10,12-Me)]2+, 6ul of a solution containing 20mM BaCl2, 80mM KCl, 12mM Spermine, 40mM Na-cacodylate pH 7, 10% v/v 2-methyl-2,4-pentanediol. Equilibrated against 1ml 35% v/v 2-methyl-2,4-pentanediol. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.7749 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7749 Å / Relative weight: 1 |
Reflection | Resolution: 0.89→17.05 Å / Num. obs: 27563 / % possible obs: 98.5 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 0.89→0.91 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.723 / Mean I/σ(I) obs: 2.2 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 0.89→17.05 Å / Cor.coef. Fo:Fc: 0.989 / Cor.coef. Fo:Fc free: 0.989 / SU B: 0.268 / SU ML: 0.007 / Cross valid method: THROUGHOUT / ESU R: 0.011 / ESU R Free: 0.011 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.688 Å2
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Refinement step | Cycle: 1 / Resolution: 0.89→17.05 Å
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Refine LS restraints |
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