5VP2
Crystal structure of the Thermus thermophilus 70S ribosome in complex with madumycin II and bound to mRNA and A-, P- and E-site tRNAs at 2.8A 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 | 2016-07-03 |
Detector | DECTRIS PILATUS 6M-F |
Wavelength(s) | 0.97950 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 209.940, 451.230, 622.440 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 155.610 - 2.800 |
R-factor | 0.2315 |
Rwork | 0.229 |
R-free | 0.27840 |
Structure solution method | MOLECULAR REPLACEMENT |
RMSD bond length | 0.003 |
RMSD bond angle | 0.652 |
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] | 155.610 | 155.610 | 2.870 |
High resolution limit [Å] | 2.800 | 12.520 | 2.800 |
Rmerge | 0.146 | 0.049 | 1.067 |
Rmeas | 0.168 | 0.055 | 1.272 |
Total number of observations | 5230080 | ||
Number of reflections | 1382659 | 14827 | 102242 |
<I/σ(I)> | 7.83 | 24.91 | 1.09 |
Completeness [%] | 96.6 | 87.4 | 97 |
Redundancy | 3.783 | 4.487 | 3.106 |
CC(1/2) | 0.987 | 0.996 | 0.239 |
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 |