+Open data
-Basic information
Entry | Database: PDB / ID: 6c8j | ||||||||||||||||||||||||||||
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Title | RNA-activated 2-AIpG monomer complex, 15 min soaking | ||||||||||||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / activated monomer | Function / homology | Chem-EQ4 / RNA / RNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 | 6c8j.cif.gz | 35.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6c8j.ent.gz | 24.4 KB | Display | PDB format |
PDBx/mmJSON format | 6c8j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/6c8j ftp://data.pdbj.org/pub/pdb/validation_reports/c8/6c8j | HTTPS FTP |
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-Related structure data
Related structure data | 6c8dC 6c8eC 6c8iC 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 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-EQ4 / #3: Chemical | ChemComp-MG / #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: 2.9 Å3/Da / Density % sol: 57.58 % |
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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 Magnesium chloride hexahydrate |
-Data collection
Diffraction | Mean temperature: 99 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Jul 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 16980 / % possible obs: 90.1 % / Redundancy: 10.6 % / CC1/2: 0.981 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.036 / Rrim(I) all: 0.116 / Χ2: 1.151 / Net I/σ(I): 12.41 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 3.76 / Num. unique obs: 1761 / CC1/2: 0.918 / Rpim(I) all: 0.189 / Rrim(I) all: 0.586 / Χ2: 0.874 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5dhc Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.235 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.088 / 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: 28.724 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→50 Å
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Refine LS restraints |
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