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- PDB-2r20: Structure of the RNA brominated tridecamer r(GCGUU-5BUGAAACGC) at... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2r20 | ||||||||||||||||||
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Title | Structure of the RNA brominated tridecamer r(GCGUU-5BUGAAACGC) at 1.3 A (Br2) | ||||||||||||||||||
![]() | RNA (5'-R(*![]() RNA / asymmetry / metal ion binding / unstacking / electrostatic | Function / homology | RNA / RNA (> 10) | ![]() Method | ![]() ![]() ![]() ![]() Timsit, Y. / Bombard, S. | ![]() ![]() Title: The 1.3 A resolution structure of the RNA tridecamer r(GCGUUUGAAACGC): Metal ion binding correlates with base unstacking and groove contraction. Authors: Timsit, Y. / Bombard, S. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 30.2 KB | Display | ![]() |
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PDB format | ![]() | 19.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 387.8 KB | Display | ![]() |
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Full document | ![]() | 387.8 KB | Display | |
Data in XML | ![]() | 5.3 KB | Display | |
Data in CIF | ![]() | 7.3 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
#1: RNA chain | Mass: 4236.421 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.35 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 5 mM MgCl2, 5 mM MnCl2, 100 mM NaCl, 30 % MPD, 50 mM tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 80 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 4, 2002 / Details: mirrors | |||||||||||||||
Radiation | Monochromator: Si (111) crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.3→20 Å / Num. all: 13060 / Num. obs: 13060 / % possible obs: 91 % / Rsym value: 4.9 / Net I/σ(I): 9.1 | |||||||||||||||
Reflection shell | Resolution: 1.3→1.45 Å / Mean I/σ(I) obs: 8.6 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Bsol: 60.67 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.936 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→20 Å
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Refine LS restraints |
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Xplor file |
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