8UD8
Crystal structure of the A2503-C2,C8-dimethylated Thermus thermophilus 70S ribosome in complex with cresomycin, mRNA, deacylated A-site tRNAphe, aminoacylated P-site fMet-tRNAmet, and deacylated E-site tRNAphe at 2.70A resolution
This is a non-PDB format compatible entry.
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 24-ID-C |
Synchrotron site | APS |
Beamline | 24-ID-C |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2022-02-23 |
Detector | DECTRIS EIGER2 X 16M |
Wavelength(s) | 0.97918 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 210.010, 449.040, 621.720 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 121.890 - 2.600 |
R-factor | 0.2182 |
Rwork | 0.216 |
R-free | 0.26130 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 8g29 |
RMSD bond length | 0.004 |
RMSD bond angle | 0.827 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | PHASER |
Refinement software | PHENIX (1.8.2) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 121.890 | 121.890 | 2.670 |
High resolution limit [Å] | 2.600 | 11.630 | 2.600 |
Rmerge | 0.166 | 0.046 | 1.739 |
Rmeas | 0.184 | 0.051 | 1.925 |
Total number of observations | 9142845 | ||
Number of reflections | 1722763 | 19181 | 128160 |
<I/σ(I)> | 8.19 | 28.88 | 0.96 |
Completeness [%] | 97.0 | 91.5 | 97.9 |
Redundancy | 5.307 | 5.61 | 5.41 |
CC(1/2) | 0.993 | 0.998 | 0.156 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION | 7.6 | 292 | 0.1-0.2 M Arginine-HCl, 0.1M Tris-HCl pH 7.6, 2.5% PEG-20K, 7-12% MPD, 0.5 mM BME |