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Yorodumi- PDB-3dw6: Crystal Structure of the Sarcin/Ricin Domain from E. COLI 23 S rR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dw6 | ||||||
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Title | Crystal Structure of the Sarcin/Ricin Domain from E. COLI 23 S rRNA, U2650-SECH3 modified | ||||||
Components | Sarcin/Ricin Domain from E. Coli 23 S rRNA | ||||||
Keywords | RNA / Sarcin Ricin Loop | ||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1 Å | ||||||
Authors | Olieric, V. / Rieder, U. / Lang, K. / Serganov, A. / Schulze-Briese, C. / Micura, R. / Dumas, P. / Ennifar, E. | ||||||
Citation | Journal: Rna / Year: 2009 Title: A fast selenium derivatization strategy for crystallization and phasing of RNA structures. Authors: Olieric, V. / Rieder, U. / Lang, K. / Serganov, A. / Schulze-Briese, C. / Micura, R. / Dumas, P. / Ennifar, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dw6.cif.gz | 44.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dw6.ent.gz | 31.3 KB | Display | PDB format |
PDBx/mmJSON format | 3dw6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dw6_validation.pdf.gz | 403.1 KB | Display | wwPDB validaton report |
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Full document | 3dw6_full_validation.pdf.gz | 403.7 KB | Display | |
Data in XML | 3dw6_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | 3dw6_validation.cif.gz | 8.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dw/3dw6 ftp://data.pdbj.org/pub/pdb/validation_reports/dw/3dw6 | HTTPS FTP |
-Related 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: 8821.241 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Chemical | ChemComp-GOL / |
#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: 1.9 Å3/Da / Density % sol: 35.27 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 3.2 M (NH4)2SO4, 50 mM K-MOPS pH 7.0, 10 mM MgCl2, 10 mM MnCl2, vapor diffusion, hanging drop, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97916 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 26, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97916 Å / Relative weight: 1 |
Reflection | Highest resolution: 1 Å / Num. obs: 64959 / % possible obs: 92.5 % / Redundancy: 6.3 % / Biso Wilson estimate: 11.318 Å2 / Rsym value: 0.054 / Net I/σ(I): 16.99 |
Reflection shell | Resolution: 1→1.1 Å / Mean I/σ(I) obs: 2.8 / Num. measured obs: 45575 / Num. unique obs: 12469 / Rsym value: 0.417 / % possible all: 71.2 |
-Processing
Software |
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Refinement | Resolution: 1→20.189 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.07 / σ(F): 1.38 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.316 Å2 / ksol: 0.46 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 41.07 Å2 / Biso mean: 13.601 Å2 / Biso min: 7.45 Å2
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Refinement step | Cycle: LAST / Resolution: 1→20.189 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23
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