+Open data
-Basic information
Entry | Database: PDB / ID: 1g2j | ||||||||||||||||||
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Title | RNA OCTAMER R(CCCP*GGGG) CONTAINING PHENYL RIBONUCLEOTIDE | ||||||||||||||||||
Components | 5'-R(*Keywords | RNA / RNA duplex / phenyl-ribonucleotide | Function / homology | RNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | Authors | Minasov, G. / Matulic-Adamic, J. / Wilds, C.J. / Haeberli, P. / Usman, N. / Beigelman, L. / Egli, M. | Citation | Journal: RNA / Year: 2000 | Title: Crystal structure of an RNA duplex containing phenyl-ribonucleotides, hydrophobic isosteres of the natural pyrimidines. Authors: Minasov, G. / Matulic-Adamic, J. / Wilds, C.J. / Haeberli, P. / Usman, N. / Beigelman, L. / Egli, M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g2j.cif.gz | 14.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g2j.ent.gz | 9.3 KB | Display | PDB format |
PDBx/mmJSON format | 1g2j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1g2j_validation.pdf.gz | 389.4 KB | Display | wwPDB validaton report |
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Full document | 1g2j_full_validation.pdf.gz | 389.4 KB | Display | |
Data in XML | 1g2j_validation.xml.gz | 3 KB | Display | |
Data in CIF | 1g2j_validation.cif.gz | 3.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/1g2j ftp://data.pdbj.org/pub/pdb/validation_reports/g2/1g2j | 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: 2523.602 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: Chemical | #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: 2.09 Å3/Da / Density % sol: 41.21 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Oligonucleotide, Calcium Acetate, Sodium Cacodylate, PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K | ||||||||||||||||||||||||||||||||||||||||
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: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→20 Å / Num. all: 1904 / Num. obs: 1904 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.6 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 1.97→2.04 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 17.3 / Num. unique all: 186 / % possible all: 99.5 |
Reflection | *PLUS Num. measured all: 25862 |
Reflection shell | *PLUS % possible obs: 99.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: RNA tetramer duplex Resolution: 1.97→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 Stereochemistry target values: G. Parkinson, J. Vojtechovsky, L. Clowney, A.T. Brunger, H.M. Berman, Acta Cryst. D, 52, 57-64 (1996). Details: Used residual target
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.97→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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