7MD7
Crystal structure of the Thermus thermophilus 70S ribosome in complex with triphenylphosphonium analog of chloramphenicol CAM-C4-TPP and protein Y (YfiA) at 2.80A 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 | 2018-07-08 |
Detector | DECTRIS PILATUS 6M-F |
Wavelength(s) | 0.97910 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 209.500, 448.640, 621.270 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 152.160 - 2.800 |
R-factor | 0.2202 |
Rwork | 0.218 |
R-free | 0.26760 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 4y4o |
RMSD bond length | 0.003 |
RMSD bond angle | 0.655 |
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] | 152.160 | 152.160 | 2.870 |
High resolution limit [Å] | 2.800 | 12.520 | 2.800 |
Rmerge | 0.201 | 0.039 | 1.507 |
Rmeas | 0.237 | 0.047 | 1.785 |
Total number of observations | 4696602 | ||
Number of reflections | 1382525 | 15550 | 101361 |
<I/σ(I)> | 6.08 | 22.54 | 0.86 |
Completeness [%] | 97.5 | 92.5 | 97.1 |
Redundancy | 3.397 | 3.401 | 3.335 |
CC(1/2) | 0.979 | 0.995 | 0.187 |
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 |