+Open data
-Basic information
Entry | Database: PDB / ID: 6cab | ||||||||||||||||||||||||||||
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Title | RNA-dGMP complex with Sr ion | ||||||||||||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / activated monomer | Function / homology | GUANOSINE-5'-MONOPHOSPHATE / STRONTIUM ION / RNA / RNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | Authors | Zhang, W. / Szostak, J.W. | Funding support | United States, 1items |
Citation | Journal: Elife / Year: 2018 | Title: Crystallographic observation of nonenzymatic RNA primer extension. Authors: Zhang, W. / Walton, T. / Li, L. / 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 | 6cab.cif.gz | 30.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cab.ent.gz | 21 KB | Display | PDB format |
PDBx/mmJSON format | 6cab.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ca/6cab ftp://data.pdbj.org/pub/pdb/validation_reports/ca/6cab | HTTPS FTP |
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-Related structure data
Related structure data | 6c8dC 6c8eC 6c8iC 6c8jC 6c8kC 6c8lC 6c8mC 6c8nC 6c8oC 5dhcS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: RNA chain | Mass: 4512.804 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-G / #3: Chemical | ChemComp-SR / #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: 2.8 Å3/Da / Density % sol: 56.3 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.040 M Sodium cacodylate trihydrate pH 7.0, 0.012 M Spermine tetrahydrochloride, 0.080 M Sodium chloride, 0.020 M Strontium chloride |
-Data collection
Diffraction | Mean temperature: 99 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Oct 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 4047 / % possible obs: 97.5 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.96 / Num. unique obs: 328 / % possible all: 82 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DHC Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 15.392 / SU ML: 0.302 / Cross valid method: THROUGHOUT / ESU R: 0.491 / ESU R Free: 0.316 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.72 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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