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- PDB-1d87: CONFORMATIONAL INFLUENCE OF THE RIBOSE 2'-HYDROXYL GROUP: CRYSTAL... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1d87 | ||||||||||||||||||
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Title | CONFORMATIONAL INFLUENCE OF THE RIBOSE 2'-HYDROXYL GROUP: CRYSTAL STRUCTURES OF DNA-RNA CHIMERIC DUPLEXES | ||||||||||||||||||
![]() | DNA/RNA (5'-R(*![]() DNA-RNA HYBRID / A-DNA/RNA / DOUBLE HELIX / DNA-RNA HYBRID COMPLEX | Function / homology | DNA/RNA hybrid | ![]() Method | ![]() ![]() Egli, M. / Usman, N. / Rich, A. | ![]() ![]() Title: Conformational influence of the ribose 2'-hydroxyl group: crystal structures of DNA-RNA chimeric duplexes. Authors: Egli, M. / Usman, N. / Rich, A. #1: ![]() Title: Large Scale Chemical Synthesis, Purification and Crystallization of RNA-DNA Chimeras Authors: Usman, N. / Egli, M. / Rich, A. #2: ![]() Title: Crystal Structure of an Okazaki Fragment at 2 Angstroms Resolution Authors: Egli, M. / Usman, N. / Zhang, S. / Rich, A. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 25.4 KB | Display | ![]() |
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PDB format | ![]() | 14.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 320 KB | Display | ![]() |
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Full document | ![]() | 344.5 KB | Display | |
Data in XML | ![]() | 4.4 KB | Display | |
Data in CIF | ![]() | 6.3 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/RNA hybrid | Mass: 3061.005 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: 2.22 Å3/Da / Density % sol: 44.49 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: pH 6.00, VAPOR DIFFUSION, SITTING DROP, temperature 291.00K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 18 ℃ / pH: 6 / Details: Egli, M., (1992) Proc.Nat.Acad.Sci.USA, 89, 534. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU AFC-5R / Detector: DIFFRACTOMETER |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2.25 Å / Num. obs: 1592 / Observed criterion σ(F): 2 |
Reflection | *PLUS Highest resolution: 2.25 Å / Observed criterion σ(F): 2 |
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Processing
Software |
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Refinement | Highest resolution: 2.25 Å / σ(F): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Highest resolution: 2.25 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor obs: 0.178 / Highest resolution: 2.25 Å / Num. reflection obs: 1592 / σ(F): 2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |