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Open data
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Basic information
Entry | Database: PDB / ID: 6u89 | ||||||||||||||||||||||||||||
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Title | RNA duplex, bound with TNA monomer | ||||||||||||||||||||||||||||
![]() | RNA (5'-R(*![]() RNA | Function / homology | Chem-TG / RNA | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() Szostak, J.W. / Zhang, W. | Funding support | | ![]()
![]() ![]() Title: Structural interpretation of the effects of threo-nucleotides on nonenzymatic template-directed polymerization. Authors: Zhang, W. / Kim, S.C. / Tam, C.P. / Lelyveld, V.S. / Bala, S. / Chaput, J.C. / 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 | ![]() | 21.2 KB | Display | ![]() |
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PDB format | ![]() | 12.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 4.3 KB | Display | |
Data in CIF | ![]() | 4.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6u7yC ![]() 6u7zC ![]() 6u8fC ![]() 6u8uC ![]() 5hbwS 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: 2245.440 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62.49 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 25 % v/v Polyethylene glycol 400, 100 mM tri-Sodium citrate; pH 5.6, 130 mM Sodium chloride, 60 mM Magnesium chloride |
-Data collection
Diffraction | Mean temperature: 99 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Jun 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: 2.36→50 Å / Num. obs: 2444 / % possible obs: 99.9 % / Redundancy: 4.5 % / CC1/2: 0.933 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.086 / Rrim(I) all: 0.185 / Χ2: 1 / Net I/σ(I): 10.67 |
Reflection shell | Resolution: 2.36→2.44 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 1.89 / Num. unique obs: 228 / CC1/2: 0.753 / Rpim(I) all: 0.307 / Rrim(I) all: 0.621 / Χ2: 0.549 / % possible all: 99.6 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 5HBW Resolution: 2.36→44.96 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 36.17 Å2
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Refinement step | Cycle: LAST / Resolution: 2.36→44.96 Å
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LS refinement shell | Resolution: 2.36→2.43 Å
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