6QQR
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with inhibitor
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | DIAMOND BEAMLINE I02 |
Synchrotron site | Diamond |
Beamline | I02 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2016-04-28 |
Detector | DECTRIS PILATUS 6M-F |
Wavelength(s) | 0.9865 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 73.780, 78.711, 86.357 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 58.173 - 1.560 |
R-factor | 0.1822 |
Rwork | 0.181 |
R-free | 0.20300 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6nvr |
RMSD bond length | 0.006 |
RMSD bond angle | 1.038 |
Data reduction software | XDS |
Data scaling software | Aimless (0.5.23) |
Phasing software | PHASER (2.5.7) |
Refinement software | PHENIX (1.9_1692) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 86.360 | 86.360 | 1.640 |
High resolution limit [Å] | 1.560 | 4.930 | 1.560 |
Rmerge | 0.036 | 0.028 | 0.781 |
Rmeas | 0.039 | 0.031 | 0.836 |
Rpim | 0.014 | 0.012 | 0.297 |
Total number of observations | 554554 | ||
Number of reflections | 72378 | 2475 | 10459 |
<I/σ(I)> | 26.3 | ||
Completeness [%] | 100.0 | 99.3 | 100 |
Redundancy | 7.7 | 6.7 | 7.8 |
CC(1/2) | 0.999 | 0.997 | 0.802 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 292 | 0.08M Sodium cacodylate pH 6.5 -7.0, 1-2 M Ammonium sulphate |