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Open data
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Basic information
Entry | Database: PDB / ID: 6c8m | |||||||||
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Title | RNA-activated 2-AIpG monomer, 1.5h soaking | |||||||||
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![]() | RNA / activated monomer | |||||||||
Function / homology | Chem-EQ1 / Chem-EQ4 / RNA / RNA (> 10)![]() | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zhang, W. / Szostak, J.W. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 35.8 KB | Display | ![]() |
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PDB format | ![]() | 24.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 7.1 KB | Display | |
Data in CIF | ![]() | 7.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6c8dC ![]() 6c8eC ![]() 6c8iC ![]() 6c8jC ![]() 6c8kC ![]() 6c8lC ![]() 6c8nC ![]() 6c8oC ![]() 6cabC ![]() 5dhcS S: Starting model for refinement 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
#1: RNA chain | Mass: 4858.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
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#2: RNA chain | Mass: 4512.804 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
#3: Chemical | ChemComp-EQ4 / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.34 % |
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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 |
-Data collection
Diffraction | Mean temperature: 99 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: May 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 4326 / % possible obs: 94.1 % / Redundancy: 2.7 % / CC1/2: 0.977 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.072 / Rrim(I) all: 0.128 / Χ2: 0.883 / Net I/σ(I): 10.64 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.732 / Mean I/σ(I) obs: 1.22 / Num. unique obs: 428 / CC1/2: 0.914 / Rpim(I) all: 0.523 / Rrim(I) all: 0.905 / Χ2: 0.503 / % possible all: 96.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5dhc Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.951 / SU B: 14.14 / SU ML: 0.273 / Cross valid method: THROUGHOUT / ESU R: 0.536 / ESU R Free: 0.298 / 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: 63.2 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→50 Å
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Refine LS restraints |
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