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Yorodumi- PDB-297d: X-RAY AND SOLUTION STUDIES OF DNA OLIGOMERS AND IMPLICATIONS FOR ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 297d | ||||||||||||||||||
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Title | X-RAY AND SOLUTION STUDIES OF DNA OLIGOMERS AND IMPLICATIONS FOR THE STRUCTURAL BASIS OF A-TRACT-DEPENDENT CURVATURE | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX / MODIFIED | Function / homology | DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å | Authors | Arbuckle, N.D. / Luisi, B.F. | Citation | Journal: J.Mol.Biol. / Year: 1997 | Title: X-ray and solution studies of DNA oligomers and implications for the structural basis of A-tract-dependent curvature. Authors: Shatzky-Schwartz, M. / Arbuckle, N.D. / Eisenstein, M. / Rabinovich, D. / Bareket-Samish, A. / Haran, T.E. / Luisi, B.F. / Shakked, Z. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 297d.cif.gz | 26.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb297d.ent.gz | 16.5 KB | Display | PDB format |
PDBx/mmJSON format | 297d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/97/297d ftp://data.pdbj.org/pub/pdb/validation_reports/97/297d | 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
#1: DNA chain | Mass: 3662.405 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 / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.18 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 277.00K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 25, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2.5 Å / Num. obs: 2427 / % possible obs: 96.8 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.062 |
Reflection shell | *PLUS % possible obs: 88 % |
-Processing
Software |
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Refinement | Resolution: 2.5→8 Å /
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Displacement parameters | Biso mean: 14.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
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Refine LS restraints |
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Software | *PLUS Name: NUCLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 8 Å / Rfactor obs: 0.22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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