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Yorodumi- PDB-1efo: CRYSTAL STRUCTURE OF AN ADENINE BULGE IN THE RNA CHAIN OF A DNA/R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1efo | ||||||
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Title | CRYSTAL STRUCTURE OF AN ADENINE BULGE IN THE RNA CHAIN OF A DNA/RNA HYBRID, D(CTCCTCTTC)/R(GAAGAGAGAG) | ||||||
Components |
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Keywords | DNA-RNA HYBRID / A-FORM CONFORMATION / HYBRID / ADENINE BULGE / LOOPED OUT / DNA-RNA COMPLEX | ||||||
Function / homology | DNA / RNA Function and homology information | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | ||||||
Authors | Sudarsanakumar, C. / Xiong, Y. / Sundaralingam, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Crystal structure of an adenine bulge in the RNA chain of a DNA.RNA hybrid, d(CTCCTCTTC).r(gaagagagag). Authors: Sudarsanakumar, C. / Xiong, Y. / Sundaralingam, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1efo.cif.gz | 18.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1efo.ent.gz | 11.8 KB | Display | PDB format |
PDBx/mmJSON format | 1efo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1efo_validation.pdf.gz | 384 KB | Display | wwPDB validaton report |
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Full document | 1efo_full_validation.pdf.gz | 384 KB | Display | |
Data in XML | 1efo_validation.xml.gz | 2.7 KB | Display | |
Data in CIF | 1efo_validation.cif.gz | 3.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/1efo ftp://data.pdbj.org/pub/pdb/validation_reports/ef/1efo | 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
#1: DNA chain | Mass: 2617.723 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: RNA chain | Mass: 3327.100 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.62 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: MPD, LITHIUM CHLORIDE, SPERMINE TETRACHLORIDE, CACODYLATE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 297 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 22, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→10 Å / Num. all: 2880 / Num. obs: 2486 / % possible obs: 91.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Rmerge(I) obs: 0.07 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4 % / Rmerge(I) obs: 0.08 / % possible all: 71.3 |
Reflection | *PLUS Num. obs: 2578 / Rmerge(I) obs: 0.069 |
Reflection shell | *PLUS % possible obs: 71.3 % |
-Processing
Software |
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Refinement | Resolution: 2.3→10 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1
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Refinement step | Cycle: LAST / Resolution: 2.3→10 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / σ(F): 2 / % reflection Rfree: 9 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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