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- PDB-1f69: CRYSTAL STRUCTURE OF THE B-DNA HEXAMER GGCGCC WITH COBALT HEXAMINE -
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Open data
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Basic information
Entry | Database: PDB / ID: 1f69 | ||||||||||||||||||
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Title | CRYSTAL STRUCTURE OF THE B-DNA HEXAMER GGCGCC WITH COBALT HEXAMINE | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / B-DNA / E-DNA / DOUBLE HELIX | Function / homology | COBALT HEXAMMINE(III) / DNA | ![]() Method | ![]() ![]() ![]() Vargason, J.M. / Eichman, B.F. / Ho, P.S. | ![]() ![]() Title: The extended and eccentric E-DNA structure induced by cytosine methylation or bromination. Authors: Vargason, J.M. / Eichman, B.F. / Ho, P.S. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 15.2 KB | Display | ![]() |
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PDB format | ![]() | 9.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 373.2 KB | Display | ![]() |
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Full document | ![]() | 373.1 KB | Display | |
Data in XML | ![]() | 2.5 KB | Display | |
Data in CIF | ![]() | 2.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: DNA chain | Mass: 1810.205 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-MG / | #3: Chemical | ChemComp-NCO / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.76 Å3/Da / Density % sol: 67.33 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: MGCL2, CO(NH3)6, SPERMINE, SODIUM CACODYLATE, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 27, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→500 Å / Num. all: 2026 / Num. obs: 2026 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Biso Wilson estimate: 42.5 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 27 |
Reflection shell | Resolution: 2.6→2.72 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.251 / % possible all: 99.9 |
Reflection | *PLUS Num. measured all: 20150 |
Reflection shell | *PLUS % possible obs: 99.9 % |
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Processing
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Refinement | Method to determine structure: ![]() Resolution: 2.6→8 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: PARKINSON ET AL.
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Refinement step | Cycle: LAST / Resolution: 2.6→8 Å
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Refine LS restraints |
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