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Open data
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Basic information
Entry | Database: PDB / ID: 5v9z | ||||||
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Title | RNA hairpin structure containing 2-MeImpG analogue bound | ||||||
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Function / homology | Chem-8OS / ![]() ![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, W. / Szostak, J.W. | ||||||
![]() | ![]() Title: Structural Rationale for the Enhanced Catalysis of Nonenzymatic RNA Primer Extension by a Downstream Oligonucleotide. Authors: Zhang, W. / Tam, C.P. / Zhou, L. / Oh, S.S. / Wang, J. / Szostak, J.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 31.2 KB | Display | ![]() |
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PDB format | ![]() | 21.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5ux3C ![]() 5uz6C ![]() 5v0hC ![]() 5v0jC ![]() 5v0oC ![]() 5vcfC ![]() 5vciC ![]() 5vgwC ![]() 6az4C ![]() 6bmdC ![]() 4fnjS 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
#1: RNA chain | Mass: 8159.974 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: RNA chain | Mass: 2485.553 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Chemical | ChemComp-8OS / |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.64 Å3/Da / Density % sol: 66.2 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 50 mM MgCl2, 3 M ammonia sulfate, 100 mM HEPES 7.5 |
-Data collection
Diffraction | Mean temperature: 99 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.5→50 Å / Num. obs: 5769 / % possible obs: 95.4 % / Redundancy: 10.6 % / CC1/2: 0.976 / Rmerge(I) obs: 0.1 / Rsym value: 0.089 / Χ2: 1.226 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 418 / CC1/2: 0.912 / Rsym value: 0.486 / Χ2: 0.678 / % possible all: 73.1 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4fnj Resolution: 2.51→43.45 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.921 / SU B: 11.619 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R: 0.312 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.171 Å2
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Refinement step | Cycle: 1 / Resolution: 2.51→43.45 Å
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Refine LS restraints |
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