+Open data
-Basic information
Entry | Database: PDB / ID: 4e8x | ||||||||||||||||||
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Title | Lambda-[Ru(TAP)2(dppz-(Me)2)]2+ bound to d(CCGGCGCCGG)2 | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / Intercalation / Photoreactive / Lambda-[Ru(TAP)2(dppz-(Me)2)]2+ | Function / homology | : / Chem-RML / DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.18 Å | Authors | Hall, J.P. / Cardin, C.J. | Citation | Journal: Thesis, University of Reading / Year: 2014 | Title: The effects of disubstitution on the binding of ruthenium complexes to DNA Authors: Hall, J.P. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4e8x.cif.gz | 17.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e8x.ent.gz | 10.9 KB | Display | PDB format |
PDBx/mmJSON format | 4e8x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4e8x_validation.pdf.gz | 732 KB | Display | wwPDB validaton report |
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Full document | 4e8x_full_validation.pdf.gz | 734.9 KB | Display | |
Data in XML | 4e8x_validation.xml.gz | 3.5 KB | Display | |
Data in CIF | 4e8x_validation.cif.gz | 4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/4e8x ftp://data.pdbj.org/pub/pdb/validation_reports/e8/4e8x | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3046.980 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: 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: 3.1 Å3/Da / Density % sol: 60.38 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1ul 2mM DNA, 1ul 2mM lambda-[Ru(TAP)2(dppz-(Me)2)]Cl2, 6ul 10% 2-methyl-2,4-pentanediol, 40mM sodium cacodylate, 12mM spermine tetra-HCl, 80mM potassium chloride, 20mM barium chloride, pH 7, ...Details: 1ul 2mM DNA, 1ul 2mM lambda-[Ru(TAP)2(dppz-(Me)2)]Cl2, 6ul 10% 2-methyl-2,4-pentanediol, 40mM sodium cacodylate, 12mM spermine tetra-HCl, 80mM potassium chloride, 20mM barium chloride, pH 7, 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: 2.18→47.09 Å / Num. all: 2219 / Num. obs: 2189 / % possible obs: 98.6 % |
Reflection shell | Resolution: 2.18→2.24 Å / % possible all: 99.3 |
-Processing
Software | Name: REFMAC / Version: 5.6.0117 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: SAD / Resolution: 2.18→33.3 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.882 / SU B: 8.752 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.272 / ESU R Free: 0.228 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 33.811 Å2
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Refinement step | Cycle: LAST / Resolution: 2.18→33.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.18→2.237 Å / Total num. of bins used: 20
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