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Yorodumi- PDB-1d65: MOLECULAR STRUCTURE OF THE B-DNA DODECAMER D(CGCAAATTTGCG)2; AN E... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d65 | ||||||||||||||||||
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Title | MOLECULAR STRUCTURE OF THE B-DNA DODECAMER D(CGCAAATTTGCG)2; AN EXAMINATION OF PROPELLER TWIST AND MINOR-GROOVE WATER STRUCTURE AT 2.2 ANGSTROMS RESOLUTION | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX | Function / homology | DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | Authors | Edwards, K.J. / Brown, D.G. / Spink, N. / Neidle, S. | Citation | Journal: J.Mol.Biol. / Year: 1992 | Title: Molecular structure of the B-DNA dodecamer d(CGCAAATTTGCG)2. An examination of propeller twist and minor-groove water structure at 2.2 A resolution. Authors: Edwards, K.J. / Brown, D.G. / Spink, N. / Skelly, J.V. / Neidle, S. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d65.cif.gz | 24.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d65.ent.gz | 15.6 KB | Display | PDB format |
PDBx/mmJSON format | 1d65.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/1d65 ftp://data.pdbj.org/pub/pdb/validation_reports/d6/1d65 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3662.404 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.02 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 289.00K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 16 ℃ / pH: 7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 292 K |
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Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418 |
Detector | Type: XENTRONICS / Detector: AREA DETECTOR |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.2 Å / Num. all: 9704 / Num. obs: 2943 |
Reflection | *PLUS Num. all: 3402 / % possible obs: 86.5 % / Num. measured all: 12896 / Rmerge(I) obs: 0.0442 |
Reflection shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.4 Å / Num. possible: 540 / Num. unique obs: 220 |
-Processing
Software | Name: NUCLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.2→8 Å / σ(I): 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(I): 2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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