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Open data
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Basic information
Entry | Database: PDB / ID: 5dhb | ||||||||||||||||||||
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Title | Cooperativity and Downstream Binding in RNA Replication | ||||||||||||||||||||
![]() | RNA (5'-R(*![]() RNA / cooperativity / monomer | Function / homology | GUANOSINE-5'-MONOPHOSPHATE / RNA | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() Zhang, W. / Fahrenbach, A.C. / Tam, C.P. / Szostak, J.W. | ![]() ![]() Title: Unusual Base-Pairing Interactions in Monomer-Template Complexes. Authors: Zhang, W. / Tam, C.P. / 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 | ![]() | 30.9 KB | Display | ![]() |
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PDB format | ![]() | 22.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 7.7 KB | Display | |
Data in CIF | ![]() | 9.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5dhcC ![]() 5hbwC ![]() 5hbxC ![]() 5hbyC ![]() 5krgC ![]() 5l00C 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: 2245.440 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-5GP / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.27 Å3/Da / Density % sol: 56.63 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Magnesium chloride hexahydrate, 30% v/v Polyethylene glycol monomethyl ether 550 |
-Data collection
Diffraction | Mean temperature: 99 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Oct 18, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→44.38 Å / Num. obs: 10344 / % possible obs: 98.3 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 29.95 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 2.13 / % possible all: 94.3 |
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Processing
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Refinement | Resolution: 1.8→44.38 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.974 / SU B: 2.94 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.1 / 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: 31.38 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→44.38 Å
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Refine LS restraints |
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