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- PDB-419d: OCTAMER 5'-R(*GP*UP*AP*UP*AP*CP*A)-D(P*C)-3' WITH SIX WATSON-CRIC... -
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Open data
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Basic information
Entry | Database: PDB / ID: 419d | ||||||||||||||||||
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Title | OCTAMER 5'-R(*GP*UP*AP*UP*AP*CP*A)-D(P*C)-3' WITH SIX WATSON-CRICK BASE-PAIRS AND TWO 3' OVERHANG RESIDUES | ||||||||||||||||||
![]() | DNA/RNA (5'-R(*![]() DNA-RNA HYBRID / HIGHLY BENT RNA / SUPERHELICES / DNA-RNA COMPLEX | Function / homology | DNA/RNA hybrid | ![]() Method | ![]() ![]() ![]() Mitra, S.M. / Shi, K. / Biswas, R. / Sundaralingam, M. | ![]() ![]() Title: The crystal structure of the octamer [r(guauaca)dC]2 with six Watson-Crick base-pairs and two 3' overhang residues. Authors: Shi, K. / Biswas, R. / Mitra, S.N. / 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 | ![]() | 26.9 KB | Display | ![]() |
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PDB format | ![]() | 17.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 367.5 KB | Display | ![]() |
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Full document | ![]() | 367.5 KB | Display | |
Data in XML | ![]() | 3.7 KB | Display | |
Data in CIF | ![]() | 4.7 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: DNA/RNA hybrid | Mass: 2494.561 Da / Num. of mol.: 4 / 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: 2.05 Å3/Da / Density % sol: 39.93 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.00 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→14.7 Å / Num. obs: 3661 / % possible obs: 81.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.037 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 8 Å / Num. obs: 3592 / % possible obs: 83.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: R(GUGCACA)DC Resolution: 2.2→8 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2
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Refine analyze | Luzzati coordinate error obs: 0.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 8 Å / Rfactor obs: 0.183 / Rfactor Rfree: 0.256 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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