6XHV
Crystal structure of the A2058-dimethylated Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A- and P-site tRNAs, and deacylated E-site tRNA at 2.40A 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 | 2020-02-09 |
Detector | DECTRIS EIGER2 X 16M |
Wavelength(s) | 0.97920 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 207.740, 444.070, 613.650 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 208.790 - 2.400 |
R-factor | 0.2395 |
Rwork | 0.237 |
R-free | 0.28570 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 4y4p |
RMSD bond length | 0.004 |
RMSD bond angle | 0.890 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | PHASER |
Refinement software | PHENIX (1.17.1_3660) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 208.790 | 208.790 | 2.460 |
High resolution limit [Å] | 2.400 | 10.730 | 2.400 |
Rmerge | 0.285 | 0.071 | 3.345 |
Rmeas | 0.295 | 0.074 | 3.493 |
Total number of observations | 32313767 | ||
Number of reflections | 2175692 | 25535 | 160010 |
<I/σ(I)> | 8.98 | 32.13 | 0.8 |
Completeness [%] | 99.9 | 99.6 | 99.7 |
Redundancy | 14.852 | 17.086 | 11.956 |
CC(1/2) | 0.992 | 0.993 | 0.111 |
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 |