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Yorodumi- PDB-438d: STRUCTURE OF AN RNA DUPLEX R(GGGCGCUCC)2 WITH NON-ADJACENT G.U BA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 438d | ||||||||||||||||||
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Title | STRUCTURE OF AN RNA DUPLEX R(GGGCGCUCC)2 WITH NON-ADJACENT G.U BASE PAIRS | ||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / A-RNA / DOUBLE HELIX / MISMATCHED | Function / homology | RNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | Authors | Shi, K. / Wahl, M.C. / Sundaralingam, M. | Citation | Journal: Nucleic Acids Res. / Year: 1999 | Title: Crystal structure of an RNA duplex r(G GCGC CC)2 with non-adjacent G*U base pairs. Authors: Shi, K. / Wahl, M. / Sundaralingam, M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 438d.cif.gz | 17.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb438d.ent.gz | 11.8 KB | Display | PDB format |
PDBx/mmJSON format | 438d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 438d_validation.pdf.gz | 363 KB | Display | wwPDB validaton report |
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Full document | 438d_full_validation.pdf.gz | 363 KB | Display | |
Data in XML | 438d_validation.xml.gz | 1.9 KB | Display | |
Data in CIF | 438d_validation.cif.gz | 2.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/38/438d ftp://data.pdbj.org/pub/pdb/validation_reports/38/438d | 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: RNA chain | Mass: 2862.759 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: 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: 2.1 Å3/Da / Density % sol: 41.5 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
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Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→10 Å / Num. all: 1521 / Num. obs: 1403 / % possible obs: 83.8 % / Observed criterion σ(F): 2 / Redundancy: 37 % / Rmerge(I) obs: 0.043 |
-Processing
Software | Name: X-PLOR / Version: 3.1 / Classification: refinement | |||||||||||||||||||||||||
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Refinement | Resolution: 2.5→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Software | *PLUS Version: 3.1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.24 / Rfactor Rwork: 0.175 / Rfactor obs: 0.196 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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