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Yorodumi- PDB-4e8s: Lambda-[Ru(TAP)2(dppz{Me2}2)]2+ bound to TCGGCGCCGA at high resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 4e8s | |||||||||||||||||||||
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Title | Lambda-[Ru(TAP)2(dppz{Me2}2)]2+ bound to TCGGCGCCGA at high resolution | |||||||||||||||||||||
Components | 5'-D(*Keywords | DNA / Intercalation / Photoreactive / Ruthenium complex | Function / homology | : / Chem-RML / DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.24 Å | Authors | Hall, J.P. / Cardin, C.J. | 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 | 4e8s.cif.gz | 29.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e8s.ent.gz | 19.6 KB | Display | PDB format |
PDBx/mmJSON format | 4e8s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/4e8s ftp://data.pdbj.org/pub/pdb/validation_reports/e8/4e8s | 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 / Details: DNA Purchased from ATDBio |
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#2: Chemical | ChemComp-BA / |
#3: Chemical | ChemComp-RML / ( |
#4: Chemical | ChemComp-CL / |
#5: 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: 2.93 Å3/Da / Density % sol: 57.97 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 1ul 2mM DNA, 1ul 2mM Lambda-[Ru(TAP)2(dppz-(Me2))]Cl2, 6ul 10% 2-methyl-2,4-pentanediol, 40mM sodium cacodylate, 12mM spermine tetra-HCl, 80mM potassium chloride, 20mM barium chloride, VAPOR ...Details: 1ul 2mM DNA, 1ul 2mM Lambda-[Ru(TAP)2(dppz-(Me2))]Cl2, 6ul 10% 2-methyl-2,4-pentanediol, 40mM sodium cacodylate, 12mM spermine tetra-HCl, 80mM potassium chloride, 20mM barium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 13, 2012 |
Radiation | Monochromator: Dual 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: 1.24→42.4 Å / Num. all: 10753 / Num. obs: 10743 / % possible obs: 99.9 % |
Reflection shell | Resolution: 1.24→1.27 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.24→29.98 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.871 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.03 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.917 Å2
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Refinement step | Cycle: LAST / Resolution: 1.24→29.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.24→1.272 Å / Total num. of bins used: 20
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