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Yorodumi- PDB-4r48: Racemic crystal structure of a calcium-bound DNA four-way junction -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r48 | ||||||||||||||||||||
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Title | Racemic crystal structure of a calcium-bound DNA four-way junction | ||||||||||||||||||||
Components | 5'-D(*Keywords | DNA / racemic DNA / racemates | Function / homology | DNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 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 | 4r48.cif.gz | 21 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r48.ent.gz | 13.4 KB | Display | PDB format |
PDBx/mmJSON format | 4r48.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/4r48 ftp://data.pdbj.org/pub/pdb/validation_reports/r4/4r48 | HTTPS FTP |
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-Related structure data
Related structure data | 4r44C 4r45C 4r47C 4r49C 4r4aC 4r4dC 1dcwS 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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: DC / Beg label comp-ID: DC / End auth comp-ID: DG / End label comp-ID: DG / Label seq-ID: 1 - 10
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Details | One crossing strand and one non-crossing strand form a continuous network in the crystal. |
-Components
#1: DNA chain | Mass: 3045.992 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA four-way junction / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-NA / | #3: Chemical | ChemComp-CA / | #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: 2.08 Å3/Da / Density % sol: 40.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1 mM DNA, 75 mM sodium cacodylate, 30 mM calcium chloride, 1 mM spermine, 35% 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: 2.33→32.91 Å / Num. all: 4365 / Num. obs: 4156 / % possible obs: 95.23 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 49.84 Å2 / Rmerge(I) obs: 0.0442 / Net I/σ(I): 4.55 |
Reflection shell | Resolution: 2.33→2.41 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2929 / Mean I/σ(I) obs: 1.68 / % possible all: 94.34 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DCW Resolution: 2.33→32.91 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.52 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||
Displacement parameters | Biso max: 79.77 Å2 / Biso mean: 46.5866 Å2 / Biso min: 25.23 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.33→32.91 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2 / % reflection obs: 99 %
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