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Open data
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Basic information
Entry | Database: PDB / ID: 6c8d | |||||||||||||||||||||||||||||||
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Title | RNA-dGMP complex with Mg ion | |||||||||||||||||||||||||||||||
![]() | RNA (5'-R(*![]() RNA / deoxyguanosine | Function / homology | 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE / RNA / RNA (> 10) | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() Zhang, W. / Szostak, J.W. | Funding support | | ![]()
![]() ![]() 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 KB | Display | ![]() |
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PDB format | ![]() | 23.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 7.5 KB | Display | |
Data in CIF | ![]() | 9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6c8eC ![]() 6c8iC ![]() 6c8jC ![]() 6c8kC ![]() 6c8lC ![]() 6c8mC ![]() 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 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-DGP / #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.69 % |
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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 PH range: 7 |
-Data collection
Diffraction | Mean temperature: 99 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 1.92→50 Å / Num. obs: 9264 / % possible obs: 99.9 % / Redundancy: 7.9 % / CC1/2: 0.964 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.056 / Rrim(I) all: 0.153 / Χ2: 1.172 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.92→1.99 Å / Redundancy: 8 % / Rmerge(I) obs: 0.722 / Mean I/σ(I) obs: 2.64 / Num. unique obs: 925 / CC1/2: 0.879 / Rpim(I) all: 0.271 / Rrim(I) all: 0.772 / Χ2: 0.882 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5DHC Resolution: 1.92→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.361 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.165 / 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: 34.07 Å2
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Refinement step | Cycle: 1 / Resolution: 1.92→50 Å
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Refine LS restraints |
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