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Yorodumi- PDB-1d92: REFINED CRYSTAL STRUCTURE OF AN OCTANUCLEOTIDE DUPLEX WITH G.T MI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d92 | ||||||||||||||||||
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Title | REFINED CRYSTAL STRUCTURE OF AN OCTANUCLEOTIDE DUPLEX WITH G.T MISMATCHED BASE-PAIRS | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / A-DNA / DOUBLE HELIX / MISMATCHED | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.25 Å | Authors | Hunter, W.N. / Kneale, G. / Brown, T. / Rabinovich, D. / Kennard, O. | Citation | Journal: J.Mol.Biol. / Year: 1986 Title: Refined crystal structure of an octanucleotide duplex with G . T mismatched base-pairs. Authors: Hunter, W.N. / Kneale, G. / Brown, T. / Rabinovich, D. / Kennard, O. #1: Journal: Nature / Year: 1985 Title: High-Resolution Structure of a DNA Helix Containing Mismatched Base Pairs Authors: Brown, T. / Kennard, O. / Kneale, G. / Rabinovich, D. #2: Journal: J.Biomol.Struct.Dyn. / Year: 1985 Title: Structural Studies of DNA Fragments. The G.T Wobble Base Pair in A, B and Z DNA. The G.A Base Pair in B-DNA Authors: Kennard, O. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d92.cif.gz | 17.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d92.ent.gz | 11.5 KB | Display | PDB format |
PDBx/mmJSON format | 1d92.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d92_validation.pdf.gz | 321.6 KB | Display | wwPDB validaton report |
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Full document | 1d92_full_validation.pdf.gz | 327.4 KB | Display | |
Data in XML | 1d92_validation.xml.gz | 2 KB | Display | |
Data in CIF | 1d92_validation.cif.gz | 2.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/1d92 ftp://data.pdbj.org/pub/pdb/validation_reports/d9/1d92 | 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: 2443.604 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: 2.59 Å3/Da / Density % sol: 52.56 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 6.5 / Details: pH 6.50, VAPOR DIFFUSION, temperature 277.00K | |||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.5 / Method: other | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 275 K |
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Detector | Type: SYNTEX P21 / Detector: DIFFRACTOMETER |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2.25 Å / Num. obs: 2414 |
Reflection | *PLUS Highest resolution: 2.25 Å / Rmerge(I) obs: 0.06 |
-Processing
Software | Name: NUCLSQ / Classification: refinement | ||||||||||||||||||||||||
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Refinement | Resolution: 2.25→10 Å / σ(I): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 2.25→10 Å
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Refinement | *PLUS Highest resolution: 2.25 Å / Lowest resolution: 10 Å / Num. reflection obs: 1924 / σ(I): 2 / Rfactor obs: 0.136 | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 85 Å2 | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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