6QR4
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 I04-1 |
Synchrotron site | Diamond |
Beamline | I04-1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2017-07-14 |
Detector | DECTRIS PILATUS 6M-F |
Wavelength(s) | 0.9159 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 74.790, 77.652, 86.845 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 57.887 - 1.520 |
R-factor | 0.1863 |
Rwork | 0.185 |
R-free | 0.20600 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6nvr |
RMSD bond length | 0.006 |
RMSD bond angle | 1.052 |
Data reduction software | XDS |
Data scaling software | Aimless (0.5.32) |
Phasing software | PHASER (2.5.7) |
Refinement software | PHENIX (1.9_1692) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 86.840 | 86.840 | 1.600 |
High resolution limit [Å] | 1.520 | 4.800 | 1.520 |
Rmerge | 0.045 | 0.043 | 0.769 |
Rmeas | 0.048 | 0.046 | 0.815 |
Rpim | 0.016 | 0.016 | 0.268 |
Number of reflections | 78938 | 2720 | 11368 |
<I/σ(I)> | 23 | ||
Completeness [%] | 100.0 | 99.8 | 100 |
Redundancy | 8.9 | 7.9 | 9.1 |
CC(1/2) | 0.999 | 0.996 | 0.853 |
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 |