+Open data
-Basic information
Entry | Database: PDB / ID: 5nbe | ||||||||||||||||||||||||||||||||||
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Title | [Ru(TAP)2(dppz-11-CN)]2+ bound to d(TCGGCGCCGA)2 | ||||||||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / Ruthenium / intercalation / asymmetric | Function / homology | : / lambda-[Ru(tap2-dppz-CN)]2+ / DNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.51 Å | Authors | McQuaid, K.T. / Hall, J.P. / Cardin, C.J. | Funding support | United Kingdom, 2items |
Citation | Journal: Chemistry / Year: 2018 | Title: X-ray Crystal Structures Show DNA Stacking Advantage of Terminal Nitrile Substitution in Ru-dppz Complexes. Authors: McQuaid, K. / Hall, J.P. / Brazier, J.A. / 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 | 5nbe.cif.gz | 22.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nbe.ent.gz | 13.4 KB | Display | PDB format |
PDBx/mmJSON format | 5nbe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/5nbe ftp://data.pdbj.org/pub/pdb/validation_reports/nb/5nbe | 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
#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-KSB / |
#3: Chemical | ChemComp-BA / |
#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: 2.74 Å3/Da / Density % sol: 55.13 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1uL 1mM dsDNA, 1ul 4mM rac[Ru(TAP)2(dppz-11-CM)]2+, 6ul of a solution containing 10% (v/v) 2-methyl-2,4-pentanediol, 80mM NaCl, 20mM Na-cacodylate pH 7, 20mM BaCl2 and 12mM spermine tetra- ...Details: 1uL 1mM dsDNA, 1ul 4mM rac[Ru(TAP)2(dppz-11-CM)]2+, 6ul of a solution containing 10% (v/v) 2-methyl-2,4-pentanediol, 80mM NaCl, 20mM Na-cacodylate pH 7, 20mM BaCl2 and 12mM spermine tetra-HCl equilibrated against 500uL 35% 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: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 20, 2016 |
Radiation | Monochromator: dual 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: 1.51→24.89 Å / Num. obs: 5452 / % possible obs: 96.7 % / Redundancy: 6.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.039 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.51→1.55 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.318 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 394 / CC1/2: 0.593 / Rpim(I) all: 0.588 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.51→24.89 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.024 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.08 / 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: 23.271 Å2
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Refinement step | Cycle: 1 / Resolution: 1.51→24.89 Å
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Refine LS restraints |
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