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Open data
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Basic information
Entry | Database: PDB / ID: 3qk4 | ||||||||||||||||||
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Title | Crystal structure of d(CGCGGGTACCCGCG)2 as A-DNA duplex | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / A-DNA duplex | Function / homology | DNA / DNA (> 10) | ![]() Method | ![]() ![]() ![]() Venkadesh, S. / Mandal, P.K. / Gautham, N. | ![]() ![]() Title: The structure of a full turn of an A-DNA duplex d(CGCGGGTACCCGCG)(2) 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 | ![]() | 27.7 KB | Display | ![]() |
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PDB format | ![]() | 17.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 380.9 KB | Display | ![]() |
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Full document | ![]() | 407.4 KB | Display | |
Data in XML | ![]() | 7.5 KB | Display | |
Data in CIF | ![]() | 9.1 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: 4282.768 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.79 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.99 Details: The drop consist of 1mM DNA, 50mM buffer, 10mM BaCl2, 1mM Spermine equilibriated against 50% MPD, pH 6.99, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 17, 2008 / Details: mirrors | |||||||||||||||
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.6→20 Å / Num. all: 2256 / Num. obs: 2171 / % possible obs: 96.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.67 % / Biso Wilson estimate: 57.76 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.0714 / Net I/σ(I): 4.5 | |||||||||||||||
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 3.71 % / Rmerge(I) obs: 0.4184 / Mean I/σ(I) obs: 1.2 / Rsym value: 0.3936 / % possible all: 95.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: A-DNA fiber Model Resolution: 2.6→19.96 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.866 / SU B: 14.13 / SU ML: 0.297 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.085 / 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: 43.531 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→19.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.602→2.669 Å / Total num. of bins used: 20
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