6QR0
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 |
Synchrotron site | Diamond |
Beamline | I04 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2017-01-28 |
Detector | DECTRIS PILATUS 6M-F |
Wavelength(s) | 0.9795 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 74.920, 77.170, 87.150 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 56.810 - 1.590 |
R-factor | 0.175 |
Rwork | 0.174 |
R-free | 0.19870 |
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 (0.5.31) |
Phasing software | PHASER (2.5.7) |
Refinement software | PHENIX (1.9_1692) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 56.810 | 56.810 | 1.630 |
High resolution limit [Å] | 1.590 | 7.110 | 1.590 |
Rmerge | 0.055 | 0.043 | 1.581 |
Rmeas | 0.058 | 0.046 | 1.677 |
Rpim | 0.019 | 0.017 | 0.549 |
Total number of observations | 603250 | ||
Number of reflections | 68585 | 877 | 4998 |
<I/σ(I)> | 19 | ||
Completeness [%] | 100.0 | 99.2 | 100 |
Redundancy | 8.8 | 7.5 | 9 |
CC(1/2) | 0.999 | 0.998 | 0.574 |
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 |