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Yorodumi- PDB-420d: CRYSTAL STRUCTURE OF A 16-MER RNA DUPLEX WITH NON-ADJACENT A(ANTI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 420d | ||||||||||||||||||
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Title | CRYSTAL STRUCTURE OF A 16-MER RNA DUPLEX WITH NON-ADJACENT A(ANTI).G(SYN) MISMATCHES | ||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / A-RNA STRUCTURE / MISMATCH A RNA | Function / homology | RNA / RNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 1.9 Å | Authors | Pan, B. / Mitra, S.N. / Sundaralingam, M. | Citation | Journal: Biochemistry / Year: 1999 | Title: Crystal structure of an RNA 16-mer duplex R(GCAGAGUUAAAUCUGC)2 with nonadjacent G(syn).A+(anti) mispairs. Authors: Pan, B. / Mitra, S.N. / Sundaralingam, M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 420d.cif.gz | 28.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb420d.ent.gz | 18.6 KB | Display | PDB format |
PDBx/mmJSON format | 420d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/20/420d ftp://data.pdbj.org/pub/pdb/validation_reports/20/420d | HTTPS FTP |
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-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: RNA chain | Mass: 5122.103 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-NA / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.47 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 27, 1997 |
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: 1.82→21.27 Å / Num. obs: 7377 / % possible obs: 87 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.073 |
Reflection | *PLUS Highest resolution: 1.82 Å / Lowest resolution: 21.27 Å / Num. obs: 5521 / % possible obs: 81 % / Observed criterion σ(F): 2 / Redundancy: 2.8 % |
Reflection shell | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 1.99 Å / % possible obs: 52.5 % |
-Processing
Software |
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Refinement | Resolution: 1.9→8 Å / Isotropic thermal model: ISOTROPIC / σ(F): 2
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Refine analyze | Luzzati coordinate error obs: 0.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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