+Open data
-Basic information
Entry | Database: PDB / ID: 6c8e | |||||||||||||||||||||||||||||||
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Title | RNA-imidazolium-bridged intermediate complex, 4h soaking | |||||||||||||||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / intermediate / dinucleotide | Function / homology | Chem-EQ1 / RNA / RNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 | 6c8e.cif.gz | 31 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6c8e.ent.gz | 21.7 KB | Display | PDB format |
PDBx/mmJSON format | 6c8e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6c8e_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6c8e_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6c8e_validation.xml.gz | 7 KB | Display | |
Data in CIF | 6c8e_validation.cif.gz | 7.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/6c8e ftp://data.pdbj.org/pub/pdb/validation_reports/c8/6c8e | HTTPS FTP |
-Related structure data
Related structure data | 6c8dC 6c8iC 6c8jC 6c8kC 6c8lC 6c8mC 6c8nC 6c8oC 6cabC 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
#1: RNA chain | Mass: 4512.804 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | #3: 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: 2.91 Å3/Da / Density % sol: 57.75 % |
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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 |
-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: Apr 4, 2017 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.8→50 Å / Num. obs: 10695 / % possible obs: 97.7 % / Redundancy: 10.1 % / CC1/2: 0.979 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.033 / Rrim(I) all: 0.103 / Χ2: 1.357 / Net I/σ(I): 20.6 | |||||||||||||||
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.713 / Mean I/σ(I) obs: 2.95 / Num. unique obs: 1051 / CC1/2: 0.984 / Rpim(I) all: 0.236 / Rrim(I) all: 0.752 / Χ2: 0.612 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DHC Resolution: 1.8→42.46 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.996 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.03 / 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: 52.894 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→42.46 Å
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Refine LS restraints |
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