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- PDB-3r86: Crystal structure of d(CCGGTACCGG)2 as B-DNA duplex grown with 5 ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3r86 | ||||||||||||||||||
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Title | Crystal structure of d(CCGGTACCGG)2 as B-DNA duplex grown with 5 mM CoCl2 | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / Duplex | Function / homology | : / DNA | ![]() Method | ![]() ![]() ![]() ![]() Venkadesh, S. / Mandal, P.K. / Gautham, N. | ![]() ![]() Title: Crystal structure of d(CCGGTACCGG)2 as B-DNA duplex Authors: Venkadesh, S. / Mandal, P.K. / Gautham, N. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 22.9 KB | Display | ![]() |
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PDB format | ![]() | 13.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 382.3 KB | Display | ![]() |
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Full document | ![]() | 402.6 KB | Display | |
Data in XML | ![]() | 6.1 KB | Display | |
Data in CIF | ![]() | 7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar 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
#1: DNA chain | Mass: 3045.992 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1mM DNA, 50mM Sodium Cacodylate buffer, 5mM CoCl2,1mM Spermine, 50% MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 7, 2010 | |||||||||||||||
Radiation | Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.604 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.8→28.4 Å / Num. all: 1410 / Num. obs: 1382 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.4 % / Biso Wilson estimate: 67.3 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.047 / Net I/σ(I): 3.7 | |||||||||||||||
Reflection shell | Resolution: 2.803→2.873 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.4 / Num. unique all: 77 / Rsym value: 0.402 / % possible all: 99 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: B-DNA fiber model Resolution: 2.8→28.37 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.934 / SU B: 21.376 / SU ML: 0.384 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.978 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→28.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.803→2.875 Å / Total num. of bins used: 20
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