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Yorodumi- PDB-188d: HYDRATION PATTERNS AND INTERMOLECULAR INTERACTIONS IN A-DNA CRYST... -
+Open data
-Basic information
Entry | Database: PDB / ID: 188d | ||||||||||||||||||
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Title | HYDRATION PATTERNS AND INTERMOLECULAR INTERACTIONS IN A-DNA CRYSTAL STRUCTURES. IMPLICATIONS FOR DNA RECOGNITION | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / A-DNA / DOUBLE HELIX | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | Authors | Eisenstein, M. / Shakked, Z. | Citation | Journal: J.Mol.Biol. / Year: 1995 Title: Hydration patterns and intermolecular interactions in A-DNA crystal structures. Implications for DNA recognition. Authors: Eisenstein, M. / Shakked, Z. #1: Journal: Acta Crystallogr.,Sect.B / Year: 1988 Title: Low-Temperature Study of the A-DNA Fragment d(GGGCGCCC) Authors: Eisenstein, M. / Hope, H. / Haran, T.E. / Frolow, F. / Shakked, Z. / Rabinovich, D. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 188d.cif.gz | 12.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb188d.ent.gz | 7.7 KB | Display | PDB format |
PDBx/mmJSON format | 188d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/88/188d ftp://data.pdbj.org/pub/pdb/validation_reports/88/188d | HTTPS FTP |
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-Related 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: 2428.593 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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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: 2.31 Å3/Da / Density % sol: 46.76 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, temperature 292.00K | |||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 115 K / Method: otherDetails: Eisenstein, M., (1988) Acta Crystallogr.,Sect.B, 44, 625. | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 115 K |
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Diffraction source | Source: ROTATING ANODE |
Detector | Type: RIGAKU AFC-5 / Detector: DIFFRACTOMETER |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 1.7 Å |
Reflection | *PLUS Highest resolution: 1.7 Å |
-Processing
Software | Name: NUCLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.2→8 Å / σ(F): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.183 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |