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Yorodumi- PDB-7jrr: Crystal structures of artificially designed homomeric RNA nanoarc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jrr | ||||||
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Title | Crystal structures of artificially designed homomeric RNA nanoarchitectures | ||||||
Components | RNA (50-MER) | ||||||
Keywords | RNA / nano structure / dimeric parallelogram | ||||||
Function / homology | : / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å | ||||||
Authors | Liu, D. / Shao, Y. / Piccirilli, J.A. / Weizmann, Y. | ||||||
Funding support | United States, 1items
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Citation | Journal: Sci Adv / Year: 2021 Title: Structures of artificially designed discrete RNA nanoarchitectures at near-atomic resolution. Authors: Liu, D. / Shao, Y. / Piccirilli, J.A. / Weizmann, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jrr.cif.gz | 42.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jrr.ent.gz | 28.5 KB | Display | PDB format |
PDBx/mmJSON format | 7jrr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/7jrr ftp://data.pdbj.org/pub/pdb/validation_reports/jr/7jrr | HTTPS FTP |
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-Related structure data
Related structure data | 7jrsC 7jrtC 2nokS 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 on special symmetry positions |
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-Components
#1: RNA chain | Mass: 16694.879 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||||
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#2: Chemical | #3: Chemical | ChemComp-MN / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-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: 49.83 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 50 mM HEPES pH 7.0, 20 of mM KCl, 5 mM of MnCl2, 35 % (v/v) MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.0879→40.22 Å / Num. obs: 10347 / % possible obs: 96.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 47.85 Å2 / CC1/2: 0.999 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 2.09→2.15 Å / Redundancy: 2.4 % / Rmerge(I) obs: 1.052 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 614 / CC1/2: 0.3 / % possible all: 77.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID: 2NOK Resolution: 2.16→28.163 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 29.08 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 109.31 Å2 / Biso mean: 57.7634 Å2 / Biso min: 27.63 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.16→28.163 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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