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- PDB-6owl: RNA oligonucleotides with 3'-arabino guanosine co-crystallized wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6owl | ||||||
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Title | RNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMP | ||||||
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![]() | RNA / arabino | ||||||
Function / homology | RNA / RNA (> 10)![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Szostak, J.W. / Kim, S. / Zhang, W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A Model for the Emergence of RNA from a Prebiotically Plausible Mixture of Ribonucleotides, Arabinonucleotides, and 2'-Deoxynucleotides. Authors: Kim, S.C. / Zhou, L. / Zhang, W. / O'Flaherty, D.K. / Rondo-Brovetto, V. / 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 | ![]() | 22 KB | Display | ![]() |
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PDB format | ![]() | 12.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 395 KB | Display | ![]() |
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Full document | ![]() | 401.7 KB | Display | |
Data in XML | ![]() | 4 KB | Display | |
Data in CIF | ![]() | 4.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6c8dS S: Starting model for refinement |
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Similar structure data |
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Links
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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.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) | ||
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#2: RNA chain | Mass: 645.454 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.08 M Sodium chloride, 0.012 M Potassium chloride, 0.02 M Magnesium chloride hexahydrate, 0.04 M Sodium cacodylate trihydrate pH 6.0, 30% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.012 M Spermine tetrahydrochloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Mar 29, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 3409 / % possible obs: 99.7 % / Redundancy: 7.1 % / CC1/2: 0.982 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.09 / Χ2: 0.831 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 332 / CC1/2: 0.94 / Rrim(I) all: 0.627 / Χ2: 0.539 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6C8D Resolution: 2→22 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.894 / SU B: 6.49 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.213 / 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: 41.933 Å2
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Refinement step | Cycle: 1 / Resolution: 2→22 Å
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Refine LS restraints |
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