7RQD
Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y, A-site deacylated tRNA analog CACCA, P-site MTI-tripeptidyl-tRNA analog ACCA-ITM, and chloramphenicol at 2.50A 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 | 2020-08-05 |
Detector | DECTRIS EIGER2 X 16M |
Wavelength(s) | 0.97895 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 209.710, 449.950, 621.200 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 224.980 - 2.500 |
R-factor | 0.2315 |
Rwork | 0.229 |
R-free | 0.27960 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 4y4o |
RMSD bond length | 0.005 |
RMSD bond angle | 0.886 |
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] | 224.980 | 224.980 | 2.560 |
High resolution limit [Å] | 2.500 | 11.180 | 2.500 |
Rmerge | 0.160 | 0.036 | 1.472 |
Rmeas | 0.180 | 0.040 | 1.685 |
Total number of observations | 9083103 | ||
Number of reflections | 1966210 | 23146 | 136889 |
<I/σ(I)> | 8.41 | 28.81 | 0.85 |
Completeness [%] | 98.5 | 98.5 | 93.1 |
Redundancy | 4.62 | 5.24 | 3.866 |
CC(1/2) | 0.990 | 0.998 | 0.160 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION | 7.6 | 292 | 0.1-0.2 M Arginine-HCl, 0.1 M Tris-HCl, pH 7.6, 2.5% PEG20000, 7-12% MPD, 0.5 mM BME |