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Yorodumi- PDB-4r45: Racemic crystal structure of a bimolecular DNA G-quadruplex (P-1) -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r45 | ||||||||||||||||||||
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Title | Racemic crystal structure of a bimolecular DNA G-quadruplex (P-1) | ||||||||||||||||||||
Components | 5'-D(*Keywords | DNA / racemic DNA / racemates | Function / homology | : / DNA / DNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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 | 4r45.cif.gz | 39.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r45.ent.gz | 29 KB | Display | PDB format |
PDBx/mmJSON format | 4r45.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/4r45 ftp://data.pdbj.org/pub/pdb/validation_reports/r4/4r45 | HTTPS FTP |
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-Related structure data
Related structure data | 4r44C 4r47C 4r48C 4r49C 4r4aC 4r4dC 2hbnS 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: 3805.460 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Bimolecular G-Quadruplex / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-K / #3: 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: 2.05 Å3/Da / Density % sol: 39.94 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 1 mM DNA, 50 mM potassium cacodylate, 40 mM potassium chloride, 50 mM magnesium chloride hexahydrate, 2.5 mM spermine, 5% v/v MPD, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 285K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Dec 23, 2013 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25.02 Å / Num. all: 9497 / Num. obs: 9011 / % possible obs: 94.89 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.7 % / Biso Wilson estimate: 49.29 Å2 / Rmerge(I) obs: 0.0628 / Net I/σ(I): 7.81 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.1227 / Mean I/σ(I) obs: 2.66 / Num. unique all: 909 / % possible all: 95.66 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2HBN Resolution: 1.9→25.02 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.861 / SU B: 4.668 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.185 / 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: 14.068 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→25.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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