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Yorodumi- PDB-246d: STRUCTURE OF THE PURINE-PYRIMIDINE ALTERNATING RNA DOUBLE HELIX, ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 246d | ||||||||||||||||||
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Title | STRUCTURE OF THE PURINE-PYRIMIDINE ALTERNATING RNA DOUBLE HELIX, R(GUAUAUA)D(C) , WITH A 3'-TERMINAL DEOXY RESIDUE | ||||||||||||||||||
Components | DNA/RNA (5'-R(*Keywords | DNA/RNA / A-DNA/RNA / DOUBLE HELIX / DNA-RNA complex | Function / homology | DNA/RNA hybrid | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | Authors | Wahl, M.C. / Ban, C. / Sekharudu, C. / Ramakrishnan, B. / Sundaralingam, M. | Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1996 | Title: Structure of the purine-pyrimidine alternating RNA double helix, r(GUAUAUA)d(C), with a 3'-terminal deoxy residue. Authors: Wahl, M.C. / Ban, C. / Sekharudu, C. / Ramakrishnan, B. / Sundaralingam, M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 246d.cif.gz | 19.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb246d.ent.gz | 12.8 KB | Display | PDB format |
PDBx/mmJSON format | 246d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 246d_validation.pdf.gz | 369.9 KB | Display | wwPDB validaton report |
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Full document | 246d_full_validation.pdf.gz | 371.6 KB | Display | |
Data in XML | 246d_validation.xml.gz | 4.1 KB | Display | |
Data in CIF | 246d_validation.cif.gz | 5.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/46/246d ftp://data.pdbj.org/pub/pdb/validation_reports/46/246d | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: DNA/RNA hybrid | Mass: 2495.545 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.18 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 291.00K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 295 K / pH: 7 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Jul 17, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.2→10 Å / Num. obs: 1775 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.0171 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 10 Å / Num. all: 2076 / % possible obs: 85.5 % / Observed criterion σ(I): 2 |
-Processing
Software |
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Refinement | Resolution: 2.2→10 Å / σ(F): 2
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 10 Å / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |