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Yorodumi- PDB-111d: CRYSTAL STRUCTURE AND STABILITY OF A DNA DUPLEX CONTAINING A(ANTI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 111d | ||||||||||||||||||
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Title | CRYSTAL STRUCTURE AND STABILITY OF A DNA DUPLEX CONTAINING A(ANTI).G(SYN) BASE-PAIRS | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX / MISMATCHED | Function / homology | DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.25 Å | Authors | Brown, T. / Leonard, G.A. / Booth, E.D. / Chambers, J. | Citation | Journal: J.Mol.Biol. / Year: 1989 | Title: Crystal structure and stability of a DNA duplex containing A(anti).G(syn) base-pairs. Authors: Brown, T. / Leonard, G.A. / Booth, E.D. / Chambers, J. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 111d.cif.gz | 21.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb111d.ent.gz | 13.1 KB | Display | PDB format |
PDBx/mmJSON format | 111d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 111d_validation.pdf.gz | 323.2 KB | Display | wwPDB validaton report |
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Full document | 111d_full_validation.pdf.gz | 334.3 KB | Display | |
Data in XML | 111d_validation.xml.gz | 2.8 KB | Display | |
Data in CIF | 111d_validation.cif.gz | 3.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/11/111d ftp://data.pdbj.org/pub/pdb/validation_reports/11/111d | HTTPS FTP |
-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: 3687.417 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: 2.29 Å3/Da / Density % sol: 46.25 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.6 Details: pH 6.60, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K | ||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.6 / Method: unknown | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Detector | Type: STOE-SIEMENS AED2 / Detector: DIFFRACTOMETER |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2.25 Å / Num. obs: 2840 / Observed criterion σ(F): 1 |
Reflection | *PLUS Highest resolution: 2.25 Å |
-Processing
Software | Name: NUCLSQ / Classification: refinement | ||||||||||||
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Refinement | Resolution: 2.25→8 Å / σ(F): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 2.25→8 Å
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Software | *PLUS Name: NUCLSQ / Classification: refinement | ||||||||||||
Refinement | *PLUS Highest resolution: 2.25 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.16 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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