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- PDB-287d: X-RAY AND SOLUTION STUDIES OF DNA OLIGOMERS AND IMPLICATIONS FOR ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 287d | ||||||||||||||||||
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Title | X-RAY AND SOLUTION STUDIES OF DNA OLIGOMERS AND IMPLICATIONS FOR THE STRUCTURAL BASIS OF A-TRACT-DEPENDENT CURVATURE | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / B-DNA / DOUBLE HELIX | Function / homology | DNA / DNA (> 10) | ![]() Method | ![]() ![]() Eisenstein, M. / Shatzky-Schwartz, M. / Shakked, Z. | ![]() ![]() Title: X-ray and solution studies of DNA oligomers and implications for the structural basis of A-tract-dependent curvature. Authors: Shatzky-Schwartz, M. / Arbuckle, N.D. / Eisenstein, M. / Rabinovich, D. / Bareket-Samish, A. / Haran, T.E. / Luisi, B.F. / Shakked, Z. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 24.6 KB | Display | ![]() |
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PDB format | ![]() | 16.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 370.7 KB | Display | ![]() |
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Full document | ![]() | 375.3 KB | Display | |
Data in XML | ![]() | 5.3 KB | Display | |
Data in CIF | ![]() | 7 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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1 |
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Unit cell |
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Components
#1: DNA chain | Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.16 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 277.00K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 6.8 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Detector | Type: RIGAKU AFC-5 / Detector: DIFFRACTOMETER |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2.2 Å / Num. obs: 2781 / % possible obs: 59.9 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.061 |
Reflection | *PLUS Highest resolution: 2.2 Å |
Reflection shell | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 2.6 Å / % possible obs: 43 % |
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Processing
Software | Name: NUCLSQ / Classification: refinement | ||||||||||||
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Refinement | Resolution: 2.2→8 Å / σ(F): 2 /
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Displacement parameters | Biso mean: 8.9 Å2 | ||||||||||||
Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 8 Å / Num. reflection all: 2781 / σ(F): 2 / Rfactor all: 0.193 / Rfactor obs: 0.15 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS Biso mean: 8.9 Å2 | ||||||||||||
Refine LS restraints | *PLUS
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