+Open data
-Basic information
Entry | Database: PDB / ID: 5krg | ||||||||||||||||||||||||||||
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Title | RNA 15mer duplex binding with PZG monomer | ||||||||||||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA | Function / homology | Chem-PZG / RNA / RNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | Authors | Zhang, W. / Tam, C.P. / Szostak, J.W. | Funding support | United States, 1items |
Citation | Journal: ACS Cent Sci / Year: 2016 | Title: Unusual Base-Pairing Interactions in Monomer-Template Complexes. Authors: Zhang, W. / Tam, C.P. / Wang, J. / 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 | 5krg.cif.gz | 49.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5krg.ent.gz | 37.9 KB | Display | PDB format |
PDBx/mmJSON format | 5krg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5krg_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 5krg_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 5krg_validation.xml.gz | 10 KB | Display | |
Data in CIF | 5krg_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kr/5krg ftp://data.pdbj.org/pub/pdb/validation_reports/kr/5krg | HTTPS FTP |
-Related structure data
Related structure data | 5dhbC 5dhcC 5hbwC 5hbxC 5hbyC 5l00C 4nfoS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: RNA chain | Mass: 4858.010 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-PZG / [( #3: Water | ChemComp-HOH / | |
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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: 2.32 Å3/Da / Density % sol: 49.5 % / Description: diamond shape |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.01 M Magnesium chloride hexahydrate, 0.05 M HEPES sodium pH 7.0, 4.0 M Lithium chloride |
-Data collection
Diffraction | Mean temperature: 99 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.97 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 21914 / % possible obs: 95.6 % / Redundancy: 4.5 % / CC1/2: 0.966 / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.18 / CC1/2: 0.941 / % possible all: 71.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NFO Resolution: 1.6→42.258 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.086 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.539 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→42.258 Å
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Refine LS restraints |
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