+Open data
-Basic information
Entry | Database: PDB / ID: 6y0y | ||||||
---|---|---|---|---|---|---|---|
Title | Sarcin Ricin Loop, mutant C2666U | ||||||
Components | RNA (27-MER) | ||||||
Keywords | RNA / ribosome | ||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 Å | ||||||
Authors | Ennifar, E. / Westhof, E. | ||||||
Citation | Journal: To Be Published Title: Sarcin Ricin Loop, mutant C2666U Authors: Ennifar, E. / Westhof, E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6y0y.cif.gz | 55.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6y0y.ent.gz | 39.8 KB | Display | PDB format |
PDBx/mmJSON format | 6y0y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y0/6y0y ftp://data.pdbj.org/pub/pdb/validation_reports/y0/6y0y | HTTPS FTP |
---|
-Related structure data
Related structure data | 3dvzS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: RNA chain | Mass: 8768.279 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) |
---|---|
#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 38.02 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 5mM MgCl2, 50mM Na HEPES pH 7.0, 25% PEG-MME 550 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9999 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 20, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 0.89→35 Å / Num. obs: 47148 / % possible obs: 99.8 % / Redundancy: 5.7 % / CC1/2: 0.998 / Net I/σ(I): 13.27 |
Reflection shell | Resolution: 0.89→0.92 Å / Num. unique obs: 2093 / CC1/2: 0.263 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DVZ Resolution: 0.95→21.281 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 15.92
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 0.8 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.95→21.281 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|