6QR3
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 | 74.870, 77.106, 86.663 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 57.606 - 1.614 |
R-factor | 0.1813 |
Rwork | 0.180 |
R-free | 0.20600 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6nvr |
RMSD bond length | 0.006 |
RMSD bond angle | 1.074 |
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] | 86.660 | 86.660 | 1.700 |
High resolution limit [Å] | 1.610 | 5.100 | 1.610 |
Rmerge | 0.111 | 0.107 | 1.276 |
Rmeas | 0.118 | 0.115 | 1.353 |
Rpim | 0.040 | 0.041 | 0.447 |
Total number of observations | 559744 | ||
Number of reflections | 65224 | 2261 | 9407 |
<I/σ(I)> | 12.8 | ||
Completeness [%] | 100.0 | 99.9 | 100 |
Redundancy | 8.6 | 7.5 | 8.8 |
CC(1/2) | 0.994 | 0.986 | 0.761 |
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 |