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Yorodumi- PDB-5ch0: Crystal structure of an A-form DNA duplex containing 5-hydroxylme... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ch0 | |||||||||||||||||||||||
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Title | Crystal structure of an A-form DNA duplex containing 5-hydroxylmethylcytidine | |||||||||||||||||||||||
Components | DNA (5'-R(*Keywords | DNA / A-form DNA duplex / 5hmC | Function / homology | DNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | Authors | Sheng, J. | Citation | Journal: To Be Published | Title: Crystal structure of an A-form DNA duplex containing 5-hydroxylmethylcytidine Authors: Sheng, J. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ch0.cif.gz | 16.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ch0.ent.gz | 8.9 KB | Display | PDB format |
PDBx/mmJSON format | 5ch0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ch0_validation.pdf.gz | 375.9 KB | Display | wwPDB validaton report |
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Full document | 5ch0_full_validation.pdf.gz | 375.9 KB | Display | |
Data in XML | 5ch0_validation.xml.gz | 3 KB | Display | |
Data in CIF | 5ch0_validation.cif.gz | 3.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ch/5ch0 ftp://data.pdbj.org/pub/pdb/validation_reports/ch/5ch0 | HTTPS FTP |
-Related structure data
Related structure data | 1z7iS 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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-Components
#1: DNA chain | Mass: 2535.603 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 46.33 % / Description: Tetragonal |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10% MPD, 40 mM Na cacodylate pH 7.0, 12 mM spermine tetra-HCl, 12mM KCl and 80 mM NaCl |
-Data collection
Diffraction | Mean temperature: 99 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.987 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 5, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 4738 / % possible obs: 99.5 % / Redundancy: 21.4 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 52.1 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 9.57 / % possible all: 92.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Z7I Resolution: 1.4→30.44 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.932 / SU B: 0.869 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.061 / 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: 7.767 Å2
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Refinement step | Cycle: 1 / Resolution: 1.4→30.44 Å
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Refine LS restraints |
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