+Open data
-Basic information
Entry | Database: PDB / ID: 6u8f | ||||||
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Title | RNA hairpin, bound with TNA monomer | ||||||
Components |
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Keywords | RNA | ||||||
Function / homology | Chem-TG / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å | ||||||
Authors | Szostak, J.W. / Zhang, W. | ||||||
Funding support | United States, 1items
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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 | 6u8f.cif.gz | 30.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6u8f.ent.gz | 19.5 KB | Display | PDB format |
PDBx/mmJSON format | 6u8f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6u8f_validation.pdf.gz | 697.3 KB | Display | wwPDB validaton report |
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Full document | 6u8f_full_validation.pdf.gz | 697.9 KB | Display | |
Data in XML | 6u8f_validation.xml.gz | 3.5 KB | Display | |
Data in CIF | 6u8f_validation.cif.gz | 4.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u8/6u8f ftp://data.pdbj.org/pub/pdb/validation_reports/u8/6u8f | HTTPS FTP |
-Related structure data
Related structure data | 6u7yC 6u7zC 6u89C 6u8uC 5vciS 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: 7098.275 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: RNA chain | Mass: 3765.256 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Chemical | ChemComp-TG / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.38 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1 M Lithium sulfate, 50 mM tri-Sodium citrate, 3 % w/v 2-Propanol, 50 mM HEPES; pH 7.5 |
-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 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: 2.8→50 Å / Num. obs: 3110 / % possible obs: 99.5 % / Redundancy: 5.4 % / CC1/2: 0.988 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.047 / Rrim(I) all: 0.111 / Χ2: 1.095 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 1.42 / Num. unique obs: 315 / CC1/2: 0.97 / Rpim(I) all: 0.304 / Rrim(I) all: 0.647 / Χ2: 0.714 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5VCI Resolution: 2.81→45.83 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 81.07 Å2
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Refinement step | Cycle: LAST / Resolution: 2.81→45.83 Å
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LS refinement shell | Resolution: 2.81→2.88 Å
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