+Open data
-Basic information
Entry | Database: PDB / ID: 4u47 | ||||||||||||||||||||
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Title | Octameric RNA duplex soaked in terbium(III)chloride | ||||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / duplex / di- and trivalent metal ions | Function / homology | TERBIUM(III) ION / RNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.952 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4u47.cif.gz | 20.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u47.ent.gz | 12.1 KB | Display | PDB format |
PDBx/mmJSON format | 4u47.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4u47_validation.pdf.gz | 380.7 KB | Display | wwPDB validaton report |
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Full document | 4u47_full_validation.pdf.gz | 380.7 KB | Display | |
Data in XML | 4u47_validation.xml.gz | 3 KB | Display | |
Data in CIF | 4u47_validation.cif.gz | 3.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u4/4u47 ftp://data.pdbj.org/pub/pdb/validation_reports/u4/4u47 | HTTPS FTP |
-Related structure data
Related structure data | 4u3lSC 4u3oC 4u3pC 4u3rC 4u78C 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 on special symmetry positions |
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-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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.26 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 28% PEG 400, 0.2 M calcium chloride, 0.002 M spermine, 0.05 M hepes sodium buffer pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.64 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 27, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.64 Å / Relative weight: 1 |
Reflection | Resolution: 1.952→32.82 Å / Num. obs: 3225 / % possible obs: 96.82 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.04999 / Net I/σ(I): 33.19 |
Reflection shell | Resolution: 1.952→2.02 Å / Redundancy: 9 % / Rmerge(I) obs: 0.4356 / Mean I/σ(I) obs: 5.35 / % possible all: 89.57 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4U3L Resolution: 1.952→32.82 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 29.08 / 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 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.952→32.82 Å
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Refine LS restraints |
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LS refinement shell |
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