+Open data
-Basic information
Entry | Database: PDB / ID: 5dhc | ||||||||||||||||||||
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Title | Cooperativity and Downstream Binding in RNA Replication | ||||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / monomer / cooperativity | Function / homology | GUANOSINE-5'-MONOPHOSPHATE / RNA / RNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | Authors | Zhang, W. / Fahrenbach, A.C. / Tam, C.P. / Szostak, J.W. | Citation | Journal: ACS Cent Sci / Year: 2016 | 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dhc.cif.gz | 60.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dhc.ent.gz | 45.1 KB | Display | PDB format |
PDBx/mmJSON format | 5dhc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/5dhc ftp://data.pdbj.org/pub/pdb/validation_reports/dh/5dhc | HTTPS FTP |
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-Related structure data
Related structure data | 5dhbC 5hbwC 5hbxC 5hbyC 5krgC 5l00C 4nfoS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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: 4483.762 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-5GP / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.6 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 10% MPD, sodium cacodylate, spermine tetrahydrochloride, strontium chloride |
-Data collection
Diffraction | Mean temperature: 99 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9795 Å |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Apr 21, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. obs: 25146 / % possible obs: 100 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 17.54 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 2.14 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NFO Resolution: 1.55→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.681 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.082 / 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: 20.59 Å2
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Refinement step | Cycle: 1 / Resolution: 1.55→50 Å
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Refine LS restraints |
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