+Open data
-Basic information
Entry | Database: PDB / ID: 4u34 | ||||||
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Title | Crystal Structures of RNA Duplexes Containing 2-thio-Uridine | ||||||
Components |
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Keywords | RNA / 2-thio-uridine | ||||||
Function / homology | RNA Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Sheng, J. / Larsen, A. / Heuberger, B. / Blain, J.C. / Szostak, J.W. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2014 Title: Crystal Structure Studies of RNA Duplexes Containing s(2)U:A and s(2)U:U Base Pairs. Authors: Sheng, J. / Larsen, A. / Heuberger, B.D. / Blain, 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 | 4u34.cif.gz | 28.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u34.ent.gz | 17.9 KB | Display | PDB format |
PDBx/mmJSON format | 4u34.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4u34_validation.pdf.gz | 387.3 KB | Display | wwPDB validaton report |
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Full document | 4u34_full_validation.pdf.gz | 387.3 KB | Display | |
Data in XML | 4u34_validation.xml.gz | 4.1 KB | Display | |
Data in CIF | 4u34_validation.cif.gz | 5.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u3/4u34 ftp://data.pdbj.org/pub/pdb/validation_reports/u3/4u34 | HTTPS FTP |
-Related structure data
Related structure data | 4u35C 4u37C 4u38C 434dS C: citing same article (ref.) S: Starting model for refinement |
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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: 2173.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: RNA chain | Mass: 2260.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 10% MPD, 40 mM Na cacodylate pH 6.0, 12 mM spermine tetra-HCl and 80 mM NaCl |
-Data collection
Diffraction | Mean temperature: 99 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 17, 2012 |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→30 Å / Num. all: 8436 / Num. obs: 8031 / % possible obs: 93.5 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 24.3 |
Reflection shell | Resolution: 1.35→1.4 Å / Redundancy: 4 % / Rmerge(I) obs: 0.129 / Mean I/σ(I) obs: 11.1 / % possible all: 66.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 434D Resolution: 1.35→22.06 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.725 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.115 Å2
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Refinement step | Cycle: 1 / Resolution: 1.35→22.06 Å
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Refine LS restraints |
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