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Open data
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Basic information
Entry | Database: PDB / ID: 6d8o | ||||||
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Title | Group I self-splicing intron P4-P6 domain mutant A230U | ||||||
![]() | Group I self-splicing intron | ||||||
![]() | RNA / ribozyme | ||||||
Function / homology | : / RNA / RNA (> 10) / RNA (> 100)![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shoffner, G.M. | ||||||
![]() | ![]() Title: In Crystallo Selection to Establish New RNA Crystal Contacts. Authors: Shoffner, G.M. / Wang, R. / Podell, E. / Cech, T.R. / Guo, F. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 376.1 KB | Display | ![]() |
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PDB format | ![]() | 284.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 410.7 KB | Display | ![]() |
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Full document | ![]() | 413.9 KB | Display | |
Data in XML | ![]() | 10.3 KB | Display | |
Data in CIF | ![]() | 14.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6bjxC ![]() 6d8lC ![]() 6d8mC ![]() 6d8nC ![]() 1gidS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: RNA chain | Mass: 51028.281 Da / Num. of mol.: 2 / Fragment: P4-P6 domain / Mutation: A230U / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #2: Chemical | ChemComp-MG / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.44 Å3/Da / Density % sol: 64.26 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 1000, sodium cacodylate, spermine |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 8, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→63.6 Å / Num. obs: 35173 / % possible obs: 99.3 % / Redundancy: 12.9 % / Biso Wilson estimate: 97.8791369622 Å2 / Net I/σ(I): 15 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1gid Resolution: 2.80112483119→59.1950080889 Å / SU ML: 0.387070124828 / Cross valid method: FREE R-VALUE / σ(F): 1.35632426171 / Phase error: 29.5202997819
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 112.264467942 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.80112483119→59.1950080889 Å
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Refine LS restraints |
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LS refinement shell |
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