+Open data
-Basic information
Entry | Database: PDB / ID: 4r4a | ||||||||||||||||||||
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Title | Racemic crystal structure of a cobalt-bound B-DNA duplex | ||||||||||||||||||||
Components | 5'-D(*Keywords | DNA / racemic DNA / racemates | Function / homology | : / SPERMINE / DNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | Authors | Mandal, P.K. / Collie, G.W. / Kauffmann, B. / Huc, I. | Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2014 | Title: Racemic DNA crystallography. Authors: Mandal, P.K. / Collie, G.W. / Kauffmann, B. / Huc, I. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r4a.cif.gz | 26.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r4a.ent.gz | 16.7 KB | Display | PDB format |
PDBx/mmJSON format | 4r4a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/4r4a ftp://data.pdbj.org/pub/pdb/validation_reports/r4/4r4a | HTTPS FTP |
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-Related structure data
Related structure data | 4r44C 4r45C 4r47C 4r48C 4r49C 4r4dC 3r86S C: citing same article (ref.) S: Starting model for refinement |
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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.: 2 / Source method: obtained synthetically / Details: B-DNA duplex / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-CO / #3: Chemical | ChemComp-SPM / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.5 mM L,D-CCGGTACCGG, 75 mM sodium cacodylate, 10 mM cobalt chloride, 1 mM spermine, 40% v/v MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9998 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 5, 2014 |
Radiation | Monochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9998 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→29.33 Å / Num. all: 14705 / Num. obs: 14025 / % possible obs: 95.38 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Biso Wilson estimate: 48.09 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 10.81 |
Reflection shell | Resolution: 1.49→1.54 Å / % possible all: 89.57 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3R86 Resolution: 1.49→29.33 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.949 / SU B: 0.839 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 12.445 Å2
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Refinement step | Cycle: LAST / Resolution: 1.49→29.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.49→1.529 Å / Total num. of bins used: 20
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