+Open data
-Basic information
Entry | Database: PDB / ID: 6jq6 | ||||||
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Title | Hatchet Ribozyme Structure soaking with Ir(NH3)6+ | ||||||
Components | RNA (81-MER) | ||||||
Keywords | RNA / ribozyme / hatchet / cleavage / catalysis / non-coding RNA | ||||||
Function / homology | IRIDIUM HEXAMMINE ION / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.626 Å | ||||||
Authors | Ren, A. / Zheng, L. | ||||||
Funding support | China, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2019 Title: Hatchet ribozyme structure and implications for cleavage mechanism. Authors: Zheng, L. / Falschlunger, C. / Huang, K. / Mairhofer, E. / Yuan, S. / Wang, J. / Patel, D.J. / Micura, R. / Ren, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jq6.cif.gz | 97.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jq6.ent.gz | 76.7 KB | Display | PDB format |
PDBx/mmJSON format | 6jq6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jq/6jq6 ftp://data.pdbj.org/pub/pdb/validation_reports/jq/6jq6 | HTTPS FTP |
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-Related 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: 26005.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: Chemical | ChemComp-IRI / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.29 Å3/Da / Density % sol: 62.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.20M K-formate, 2.2M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.103 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 2, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.103 Å / Relative weight: 1 |
Reflection | Resolution: 2.61→50 Å / Num. obs: 19049 / % possible obs: 99 % / Redundancy: 20 % / Rpim(I) all: 0.041 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 2.61→2.72 Å / Num. unique obs: 683 / Rpim(I) all: 2.29 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.626→50 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.28
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.626→50 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -0.7861 Å / Origin y: 33.19 Å / Origin z: 55.7008 Å
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Refinement TLS group | Selection details: all |