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Yorodumi- PDB-220d: INFLUENCE OF COUNTER-IONS ON THE CRYSTAL STRUCTURES OF DNA DECAME... -
+Open data
-Basic information
Entry | Database: PDB / ID: 220d | ||||||||||||||||||
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Title | INFLUENCE OF COUNTER-IONS ON THE CRYSTAL STRUCTURES OF DNA DECAMERS: BINDING OF [CO(NH3)6]3+ AND BA2+ TO A-DNA | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / A-DNA / DOUBLE HELIX | Function / homology | : / DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2 Å | Authors | Gao, Y.-G. / Robinson, H. / Van Boom, J.H. / Wang, A.H.-J. | Citation | Journal: Biophys.J. / Year: 1995 | Title: Influence of counter-ions on the crystal structures of DNA decamers: binding of [Co(NH3)6]3+ and Ba2+ to A-DNA. Authors: Gao, Y.G. / Robinson, H. / van Boom, J.H. / Wang, A.H. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 220d.cif.gz | 17 KB | Display | PDBx/mmCIF format |
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PDB format | pdb220d.ent.gz | 9.7 KB | Display | PDB format |
PDBx/mmJSON format | 220d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 220d_validation.pdf.gz | 320.9 KB | Display | wwPDB validaton report |
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Full document | 220d_full_validation.pdf.gz | 334.4 KB | Display | |
Data in XML | 220d_validation.xml.gz | 3.2 KB | Display | |
Data in CIF | 220d_validation.cif.gz | 4.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/20/220d ftp://data.pdbj.org/pub/pdb/validation_reports/20/220d | 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
#1: DNA chain | Mass: 3045.992 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Chemical | ChemComp-BA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.78 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 6.5 / Details: pH 6.50, VAPOR DIFFUSION | |||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: unknown | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Ambient temp details: ROOM TEMPERATURE |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2 Å / Num. obs: 1817 |
Reflection | *PLUS Rmerge(I) obs: 0.065 |
-Processing
Software | Name: NUCLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Highest resolution: 2 Å / σ(F): 4 /
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Refinement step | Cycle: LAST / Highest resolution: 2 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2 Å / σ(F): 4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |