+Open data
-Basic information
Entry | Database: PDB / ID: 4ms5 | ||||||
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Title | Lambda-[Ru(TAP)2(dppz-11,12-(F)2)]2+ bound to CCGGATCCGG | ||||||
Components | DNA | ||||||
Keywords | DNA / Intercalation / semi-intercalation / ruthenium | ||||||
Function / homology | : / Chem-RKF / DNA Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 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 | 4ms5.cif.gz | 17.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ms5.ent.gz | 10.3 KB | Display | PDB format |
PDBx/mmJSON format | 4ms5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ms5_validation.pdf.gz | 748.9 KB | Display | wwPDB validaton report |
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Full document | 4ms5_full_validation.pdf.gz | 752.1 KB | Display | |
Data in XML | 4ms5_validation.xml.gz | 3.2 KB | Display | |
Data in CIF | 4ms5_validation.cif.gz | 3.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ms/4ms5 ftp://data.pdbj.org/pub/pdb/validation_reports/ms/4ms5 | HTTPS FTP |
-Related structure data
Related structure data | 4e8xC 4e95C 3qrnS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 3045.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA synthesised by ATDBio |
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#2: Chemical | ChemComp-BA / |
#3: Chemical | ChemComp-RKF / ( |
#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: 3.22 Å3/Da / Density % sol: 61.78 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: 1ul 1mM (CCGGATCCGG)2, 1ul 2mM Ru(TAP)2(dppz-11,12-(F)2]Cl2, 6ul of 40mM Na-cacodylate, 12mM spermine, 20mM BaCl2, 80mM KCl, 10% 2-methyl-2,4-pentanediol. Equilibriated against 1ml 35% 2- ...Details: 1ul 1mM (CCGGATCCGG)2, 1ul 2mM Ru(TAP)2(dppz-11,12-(F)2]Cl2, 6ul of 40mM Na-cacodylate, 12mM spermine, 20mM BaCl2, 80mM KCl, 10% 2-methyl-2,4-pentanediol. Equilibriated against 1ml 35% 2-methyl-2,4-pentanediol, pH 6.3, 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: 0.8266 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2012 |
Radiation | Monochromator: dual Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8266 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→34.6 Å / Num. all: 2136 / Num. obs: 2136 / % possible obs: 99 % / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.23→2.29 Å / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3QRN Resolution: 2.23→28.01 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.941 / SU B: 8.526 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.205 / 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: 36.835 Å2
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Refinement step | Cycle: LAST / Resolution: 2.23→28.01 Å
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Refine LS restraints |
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