+Open data
-Basic information
Entry | Database: PDB / ID: 138d | ||||||||||||||||||
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Title | A-DNA DECAMER D(GCGGGCCCGC)-HEXAGONAL CRYSTAL FORM | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / A-DNA / DOUBLE HELIX | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | Authors | Ramakrishnan, B. / Sundaralingam, M. | Citation | Journal: Biochemistry / Year: 1993 | Title: Evidence for crystal environment dominating base sequence effects on DNA conformation: crystal structures of the orthorhombic and hexagonal polymorphs of the A-DNA decamer d(GCGGGCCCGC) and ...Title: Evidence for crystal environment dominating base sequence effects on DNA conformation: crystal structures of the orthorhombic and hexagonal polymorphs of the A-DNA decamer d(GCGGGCCCGC) and comparison with their isomorphous crystal structures. Authors: Ramakrishnan, B. / Sundaralingam, M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 138d.cif.gz | 14.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb138d.ent.gz | 9 KB | Display | PDB format |
PDBx/mmJSON format | 138d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 138d_validation.pdf.gz | 359.1 KB | Display | wwPDB validaton report |
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Full document | 138d_full_validation.pdf.gz | 360.6 KB | Display | |
Data in XML | 138d_validation.xml.gz | 2.9 KB | Display | |
Data in CIF | 138d_validation.cif.gz | 3.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/38/138d ftp://data.pdbj.org/pub/pdb/validation_reports/38/138d | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3046.980 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.15 % | ||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: ROTATING ANODE |
Detector | Type: SIEMENS / Detector: AREA DETECTOR |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.8→15 Å / Num. obs: 3435 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 15 Å / % possible obs: 91 % / Num. measured all: 19222 / Rmerge(I) obs: 0.039 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.8→8 Å / σ(F): 3 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 1.8→8 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 8 Å / Num. reflection obs: 2298 / σ(F): 3 / Rfactor obs: 0.183 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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