+Open data
-Basic information
Entry | Database: PDB / ID: 6u8u | ||||||||||||||||||||||||||||
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Title | RNA duplex bound with TNA 3'-3' imidazolium dimer | ||||||||||||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA | Function / homology | Chem-Q1V / RNA / RNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | Authors | Szostak, J.W. / Zhang, W. | Funding support | United States, 1items |
Citation | Journal: Nucleic Acids Res. / Year: 2021 | 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6u8u.cif.gz | 31.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6u8u.ent.gz | 21 KB | Display | PDB format |
PDBx/mmJSON format | 6u8u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u8/6u8u ftp://data.pdbj.org/pub/pdb/validation_reports/u8/6u8u | HTTPS FTP |
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-Related structure data
Related structure data | 6u7yC 6u7zC 6u89C 6u8fC 6c8dS 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
#1: RNA chain | Mass: 4512.804 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.45 Å3/Da / Density % sol: 49.7 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 10 % w/v Polyethylene glycol 6,000, 50 mM HEPES; pH 7.0, 200 mM Ammonium acetate, 150 mM Magnesium acetate |
-Data collection
Diffraction | Mean temperature: 99 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Jun 15, 2018 |
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: 4009 / % possible obs: 99.9 % / Redundancy: 10.2 % / CC1/2: 1 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.02 / Rrim(I) all: 0.06 / Χ2: 0.818 / Net I/σ(I): 37.2 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 387 / CC1/2: 0.958 / Rpim(I) all: 0.228 / Rrim(I) all: 0.745 / Χ2: 0.566 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6C8D Resolution: 2.4→50 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 53.86 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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LS refinement shell | Resolution: 2.4→2.46 Å
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