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Open data
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Basic information
Entry | Database: PDB / ID: 4u3l | ||||||||||||||||||||
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Title | octameric RNA duplex co-crystallized in calcium(II)chloride | ||||||||||||||||||||
![]() | RNA (5'-R(*![]() RNA / duplex / di- and trivalent metal ions | Function / homology | 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 | ![]() | 20.6 KB | Display | ![]() |
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PDB format | ![]() | 12.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 390.5 KB | Display | ![]() |
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Full document | ![]() | 390.4 KB | Display | |
Data in XML | ![]() | 3.3 KB | Display | |
Data in CIF | ![]() | 4.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 2.25 Å3/Da / Density % sol: 45.22 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 28% PEG 400, 0.2 M calcium chloride, 0.002 M spermine, 0.05 hepes sodium buffer pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 27, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.61 Å / Relative weight: 1 |
Reflection | Resolution: 1.482→32.3 Å / Num. obs: 14194 / % possible obs: 99.84 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 25.82 |
Reflection shell | Resolution: 1.482→1.535 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.47 / % possible all: 99.45 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 1.482→32.305 Å
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Refine LS restraints |
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LS refinement shell |
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