+Open data
-Basic information
Entry | Database: PDB / ID: 281d | ||||||||||||||||||
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Title | CRYSTAL STRUCTURE OF THE A-DNA OCTAMER D(GGCATGCC) | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / A-DNA / DOUBLE HELIX | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.38 Å | Authors | Nunn, C.M. / Neidle, S. | Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1997 | Title: Structure of the A-DNA octamer d(GGCATGCC). Authors: Nunn, C.M. / Neidle, S. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 281d.cif.gz | 17.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb281d.ent.gz | 11.1 KB | Display | PDB format |
PDBx/mmJSON format | 281d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 281d_validation.pdf.gz | 319.5 KB | Display | wwPDB validaton report |
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Full document | 281d_full_validation.pdf.gz | 320 KB | Display | |
Data in XML | 281d_validation.xml.gz | 1.3 KB | Display | |
Data in CIF | 281d_validation.cif.gz | 2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/81/281d ftp://data.pdbj.org/pub/pdb/validation_reports/81/281d | 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: 2427.605 Da / Num. of mol.: 2 / Source method: isolated from a natural source #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: 2.74 Å3/Da / Density % sol: 55.06 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7 Details: pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 287.00K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 287 K / pH: 7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
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Detector | Type: XENTRONICS / Detector: AREA DETECTOR / Date: Jan 11, 1996 |
Radiation | Monochromator: GRAPHITE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.38 Å / Num. all: 5252 / Num. obs: 2167 / % possible obs: 97 % / Rmerge(I) obs: 0.039 |
Reflection | *PLUS Highest resolution: 2.38 Å / Num. all: 2167 / Num. obs: 2104 / % possible obs: 97 % / Num. measured all: 5252 |
-Processing
Software |
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Refinement | Resolution: 2.38→8 Å / σ(F): 2 /
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Displacement parameters | Biso mean: 26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 2.38→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.38 Å / Lowest resolution: 8 Å / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 26 Å2 |