+Open data
-Basic information
Entry | Database: PDB / ID: 402d | ||||||||||||||||||
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Title | 5'-R(*CP*GP*CP*CP*AP*GP*CP*G)-3' | ||||||||||||||||||
Components | RNA(5'-R(*Keywords | RNA / RNA DOUBLE HELIX / RNA WITH TANDEM C-A+ BASE PAIR | Function / homology | RNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | Authors | Jang, S.B. / Hung, L.-W. / Chi, Y.-I. / Holbrook, E.L. / Carter, R. / Holbrook, S.R. | Citation | Journal: Biochemistry / Year: 1998 | Title: Structure of an RNA internal loop consisting of tandem C-A+ base pairs. Authors: Jang, S.B. / Hung, L.W. / Chi, Y.I. / Holbrook, E.L. / Carter, R.J. / Holbrook, S.R. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 402d.cif.gz | 16.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb402d.ent.gz | 11.1 KB | Display | PDB format |
PDBx/mmJSON format | 402d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 402d_validation.pdf.gz | 379.8 KB | Display | wwPDB validaton report |
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Full document | 402d_full_validation.pdf.gz | 379.8 KB | Display | |
Data in XML | 402d_validation.xml.gz | 2.8 KB | Display | |
Data in CIF | 402d_validation.cif.gz | 3.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/02/402d ftp://data.pdbj.org/pub/pdb/validation_reports/02/402d | 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: RNA chain | Mass: 2540.593 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: 2.16 Å3/Da / Density % sol: 42.7 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5.5 / Details: pH 5.50, VAPOR DIFFUSION, HANGING DROP | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal | *PLUS Density % sol: 42.7 % | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: drop solution was mixed with an equal volume of reservoir solution | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 2101 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 11.9 % / Rmerge(I) obs: 0.044 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 30 Å / % possible obs: 96.8 % / Num. measured all: 25094 |
Reflection shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.38 Å / % possible obs: 80.2 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 4.5 |
-Processing
Software |
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Refinement | Resolution: 2.3→8 Å / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 10000 / Isotropic thermal model: ISOTROPIC / σ(F): 2.5
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Solvent computation | Solvent model: BULK SOLVENT / Bsol: 57.1 Å2 / ksol: 0.45 e/Å3 | ||||||||||||||||||||
Refine Biso | Class: 1 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
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Xplor file | Serial no: 1 / Param file: DNA_RNA_REP.PARAM WATER_R | ||||||||||||||||||||
Software | *PLUS Name: 'CNS' / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 8 Å / σ(F): 2.5 / % reflection Rfree: 10 % / Num. reflection obs: 2030 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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