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Yorodumi- PDB-218d: THE STRUCTURE OF A NEW CRYSTAL FORM OF A DNA DODECAMER CONTAINING... -
+Open data
-Basic information
Entry | Database: PDB / ID: 218d | ||||||||||||||||||
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Title | THE STRUCTURE OF A NEW CRYSTAL FORM OF A DNA DODECAMER CONTAINING T.(O6ME)G BASE PAIRS | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX / MODIFIED / MISMATCHED | Function / homology | DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.25 Å | Authors | Vojtechovsky, J. / Eaton, M.D. / Gaffney, B. / Jones, R. / Berman, H.M. | Citation | Journal: Biochemistry / Year: 1995 | Title: Structure of a new crystal form of a DNA dodecamer containing T.(O6Me)G base pairs. Authors: Vojtechovsky, J. / Eaton, M.D. / Gaffney, B. / Jones, R. / Berman, H.M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 218d.cif.gz | 23.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb218d.ent.gz | 15.6 KB | Display | PDB format |
PDBx/mmJSON format | 218d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/18/218d ftp://data.pdbj.org/pub/pdb/validation_reports/18/218d | 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: 3692.430 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: 1.87 Å3/Da / Density % sol: 34.36 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7 Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 296.00K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 23 ℃ | ||||||||||||||||||||||||||||||||||||||||||
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: ENRAF-NONIUS FR571 |
Detector | Type: ENRAF-NONIUS CAD4 / Detector: DIFFRACTOMETER |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 1.97 Å / Num. all: 4218 / Num. obs: 2387 / % possible obs: 99.5 % / Observed criterion σ(F): 2 |
Reflection | *PLUS Highest resolution: 1.97 Å / % possible obs: 99.5 % / Observed criterion σ(F): 2 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.25→10 Å / σ(F): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 2.25→10 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.25 Å / Lowest resolution: 10 Å / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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