8VTX
Crystal structure of the A2058-N6-dimethylated Thermus thermophilus 70S ribosome in complex with macrolone MCX-128, mRNA, aminoacylated A-site Phe-tRNAphe, aminoacylated P-site fMet-tRNAmet, and deacylated E-site tRNAphe 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 | 2020-10-24 |
Detector | DECTRIS EIGER2 X 16M |
Wavelength(s) | 0.97911 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 209.540, 448.510, 620.520 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 147.200 - 2.400 |
R-factor | 0.2216 |
Rwork | 0.220 |
R-free | 0.25950 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6xhv |
RMSD bond length | 0.005 |
RMSD bond angle | 0.916 |
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] | 147.200 | 147.200 | 2.460 |
High resolution limit [Å] | 2.400 | 10.730 | 2.400 |
Rmerge | 0.170 | 0.060 | 1.672 |
Rmeas | 0.187 | 0.067 | 1.830 |
Total number of observations | 13389343 | ||
Number of reflections | 2227511 | 25556 | 163896 |
<I/σ(I)> | 8.15 | 24.54 | 1.04 |
Completeness [%] | 99.3 | 96.9 | 99.1 |
Redundancy | 6.011 | 6.268 | 5.916 |
CC(1/2) | 0.990 | 0.992 | 0.201 |
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 |