+Open data
-Basic information
Entry | Database: PDB / ID: 3u38 | ||||||||||||||||||
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Title | Intercalation of lambda-[Ru(phen)2(dppz)]2+ into d(CCGGTACCGG)2 | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / B-DNA / Ruthenium | Function / homology | : / Lambda-Ru(phen)2(dppz) complex / DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.13 Å | Authors | Cardin, C.J. / Hall, J.P. / Niyazi, H. | Citation | Journal: Nat Chem / Year: 2012 | Title: Crystal structures of lambda-[Ru(phen)2dppz]2+ with oligonucleotides containing TA/TA and AT/AT steps show two intercalation modes Authors: Niyazi, H. / Hall, J.P. / O'Sullivan, K. / Winter, G. / Sorensen, T. / Kelly, J.M. / 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 | 3u38.cif.gz | 19.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u38.ent.gz | 12.8 KB | Display | PDB format |
PDBx/mmJSON format | 3u38.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3u38_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3u38_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3u38_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | 3u38_validation.cif.gz | 4.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u3/3u38 ftp://data.pdbj.org/pub/pdb/validation_reports/u3/3u38 | 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 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: Oligo purchased from ATD Bio | ||||
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#2: Chemical | #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: 3.68 Å3/Da / Density % sol: 66.54 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 40mM pH 7 sodium cacodylate, 12mM spermine, 20mM BaCl2, 10% 2-methyl-2,4-pentanediol, 1mM oligonuclotide, 3mM lambda-[Ru(phenanthroline)2dipyridophenazine]Cl2, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9464 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 19, 2011 |
Radiation | Monochromator: Dual Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9464 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→52.55 Å / Num. all: 2908 / Num. obs: 2783 / % possible obs: 95.7 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.1→2.16 Å / % possible all: 100 |
-Processing
Software | Name: REFMAC / Version: 5.6.0117 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: SAD / Resolution: 2.13→14.86 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.027 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 40.415 Å2
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Refinement step | Cycle: LAST / Resolution: 2.13→14.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.133→2.187 Å / Total num. of bins used: 20
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