+Open data
-Basic information
Entry | Database: PDB / ID: 4u3p | |||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Octameric RNA duplex co-crystallized with strontium(II)chloride | |||||||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / duplex / di- and trivalent metal ions | Function / homology | STRONTIUM ION / RNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.866 Å | Authors | Schaffer, M.F. / Spingler, B. / Schnabl, J. / Peng, G. / Olieric, V. / Sigel, R.K.O. | Citation | Journal: Int J Mol Sci / Year: 2016 | Title: The X-ray Structures of Six Octameric RNA Duplexes in the Presence of Different Di- and Trivalent Cations. Authors: Schaffer, M.F. / Peng, G. / Spingler, B. / Schnabl, J. / Wang, M. / Olieric, V. / Sigel, R.K. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4u3p.cif.gz | 22.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4u3p.ent.gz | 13.3 KB | Display | PDB format |
PDBx/mmJSON format | 4u3p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u3/4u3p ftp://data.pdbj.org/pub/pdb/validation_reports/u3/4u3p | HTTPS FTP |
---|
-Related structure data
Related structure data | 4u3lSC 4u3oC 4u3rC 4u47C 4u78C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||
Components on special symmetry positions |
|
-Components
#1: RNA chain | Mass: 2526.561 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.14 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 28% PEG 8000, 0.2 M strontium chloride, 0.2 M ammonium acetate, 0.01 M magnesium acetate, 0.05 M sodium cacodylate buffer pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.6 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 31, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.6 Å / Relative weight: 1 |
Reflection | Resolution: 1.866→32.58 Å / Num. obs: 3728 / % possible obs: 99.79 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.03566 / Net I/σ(I): 34.84 |
Reflection shell | Resolution: 1.866→1.932 Å / Redundancy: 7 % / Rmerge(I) obs: 0.4714 / Mean I/σ(I) obs: 4.06 / % possible all: 97.96 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4U3L Resolution: 1.866→32.58 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.7 / Phase error: 27.74 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.866→32.58 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|