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Yorodumi- PDB-6zyb: Sarcin-Ricin Loop RNA from Ecoli with a C2667-2'-OCF3 modification -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zyb | ||||||||||||
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Title | Sarcin-Ricin Loop RNA from Ecoli with a C2667-2'-OCF3 modification | ||||||||||||
Components | Sarcin-Ricin Loop RNA from Ecoli with a C2667-2'-OCF3 modification | ||||||||||||
Keywords | RNA / Ribosome / modification | ||||||||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||||||||
Biological species | synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.9 Å | ||||||||||||
Authors | Ennifar, E. | ||||||||||||
Funding support | Austria, 3items
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Citation | Journal: Chem Sci / Year: 2020 Title: 2'- O -Trifluoromethylated RNA - a powerful modification for RNA chemistry and NMR spectroscopy. Authors: Himmelstoss, M. / Erharter, K. / Renard, E. / Ennifar, E. / Kreutz, C. / Micura, R. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zyb.cif.gz | 68.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zyb.ent.gz | 43.5 KB | Display | PDB format |
PDBx/mmJSON format | 6zyb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zyb_validation.pdf.gz | 399.4 KB | Display | wwPDB validaton report |
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Full document | 6zyb_full_validation.pdf.gz | 399.5 KB | Display | |
Data in XML | 6zyb_validation.xml.gz | 5.4 KB | Display | |
Data in CIF | 6zyb_validation.cif.gz | 7.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zy/6zyb ftp://data.pdbj.org/pub/pdb/validation_reports/zy/6zyb | HTTPS FTP |
-Related structure data
Related structure data | 6zxzC 3dvzS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 8796.253 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) |
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#2: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.27 % / Description: platelet |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 3.2 M ammonium sulfate, 50 mM potassium MOPS, pH 7.0, 10 mM magnesium chloride, 10 mM manganese chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 24, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 0.9→35 Å / Num. obs: 96381 / % possible obs: 100 % / Redundancy: 39.1 % / Biso Wilson estimate: 11.06 Å2 / CC1/2: 1 / Net I/σ(I): 45 |
Reflection shell | Resolution: 0.9→0.92 Å / Num. unique obs: 3626 / CC1/2: 0.555 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DVZ Resolution: 0.9→29.5 Å / SU ML: 0.1305 / Cross valid method: FREE R-VALUE / σ(F): 1.09 / Phase error: 18.221 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0 Å / VDW probe radii: 0.3 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.49 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.9→29.5 Å
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Refine LS restraints |
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LS refinement shell |
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