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Yorodumi- PDB-1d28: CRYSTAL AND MOLECULAR STRUCTURE OF A DNA FRAGMENT: D(CGTGAATTCACG) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d28 | ||||||||||||||||||
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Title | CRYSTAL AND MOLECULAR STRUCTURE OF A DNA FRAGMENT: D(CGTGAATTCACG) | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX | Function / homology | DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.7 Å | Authors | Narayana, N. / Ginell, S.L. / Russu, I.M. / Berman, H.M. | Citation | Journal: Biochemistry / Year: 1991 | Title: Crystal and molecular structure of a DNA fragment: d(CGTGAATTCACG). Authors: Narayana, N. / Ginell, S.L. / Russu, I.M. / 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 | 1d28.cif.gz | 24.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d28.ent.gz | 15 KB | Display | PDB format |
PDBx/mmJSON format | 1d28.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/1d28 ftp://data.pdbj.org/pub/pdb/validation_reports/d2/1d28 | 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: 2.27 Å3/Da / Density % sol: 45.79 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 277.00K | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 183 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 |
Detector | Type: SIEMENS-NICOLET / Detector: AREA DETECTOR |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2.1 Å / Num. obs: 2075 / Observed criterion σ(I): 2 |
Reflection | *PLUS Highest resolution: 2.1 Å / % possible obs: 56 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.0875 |
-Processing
Software | Name: NUCLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.7→10 Å / σ(I): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 2.7→10 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 10 Å / σ(I): 2 / Rfactor obs: 0.17 / Num. reflection obs: 1532 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |