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- PDB-116d: CRYSTAL AND MOLECULAR STRUCTURE OF THE A-DNA DODECAMER D(CCGTACGT... -
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Open data
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Basic information
Entry | Database: PDB / ID: 116d | ||||||||||||||||||
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Title | CRYSTAL AND MOLECULAR STRUCTURE OF THE A-DNA DODECAMER D(CCGTACGTACGG): CHOICE OF FRAGMENT HELICAL AXIS | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / A-DNA / DOUBLE HELIX | Function / homology | DNA / DNA (> 10) | ![]() Method | ![]() ![]() Bingman, C.A. / Zon, G. / Sundaralingam, M. | ![]() ![]() Title: Crystal and molecular structure of the A-DNA dodecamer d(CCGTACGTACGG). Choice of fragment helical axis. Authors: Bingman, C.A. / Zon, G. / Sundaralingam, M. #1: ![]() Title: Crystal and Molecular Structure of the Alternating Dodecamer d(GCGTACGTACGC) in the A-DNA Form: Comparison with the Isomorphous Non-Alternating Dodecamer d(CCGTACGTACGG) Authors: Bingman, C.A. / Jain, S. / Zon, G. / Sundaralingam, M. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 16.6 KB | Display | ![]() |
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PDB format | ![]() | 9.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 365.2 KB | Display | ![]() |
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Full document | ![]() | 368.9 KB | Display | |
Data in XML | ![]() | 3.4 KB | Display | |
Data in CIF | ![]() | 4.2 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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1 | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 3663.392 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.09 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 6.5 / Details: pH 6.50, VAPOR DIFFUSION | ||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.5 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Detector | Type: ENRAF-NONIUS / Detector: OSCILLATION CAMERA |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2.5 Å / Num. all: 4971 / Num. obs: 1664 / Observed criterion σ(I): 2 |
Reflection | *PLUS Highest resolution: 2.5 Å / Observed criterion σ(I): 2 / Num. measured all: 4971 / Rmerge(I) obs: 0.04 |
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Processing
Software | Name: NUCLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.5→8 Å / σ(F): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 8 Å / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |