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Open data
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Basic information
Entry | Database: PDB / ID: 4u3p | |||||||||||||||||||||||
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Title | Octameric RNA duplex co-crystallized with strontium(II)chloride | |||||||||||||||||||||||
![]() | RNA (5'-R(*![]() RNA / duplex / di- and trivalent metal ions | Function / homology | STRONTIUM ION / RNA | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() Schaffer, M.F. / Spingler, B. / Schnabl, J. / Peng, G. / Olieric, V. / Sigel, R.K.O. | ![]() ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 22.1 KB | Display | ![]() |
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PDB format | ![]() | 13.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4u3lSC ![]() 4u3oC ![]() 4u3rC ![]() 4u47C ![]() 4u78C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.14 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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
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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: 1.866→32.58 Å
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Refine LS restraints |
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LS refinement shell |
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