6QR2
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 I03 |
Synchrotron site | Diamond |
Beamline | I03 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2017-03-11 |
Detector | DECTRIS PILATUS3 6M |
Wavelength(s) | 0.9763 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 74.881, 76.728, 86.588 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 38.364 - 1.550 |
R-factor | 0.1694 |
Rwork | 0.169 |
R-free | 0.18210 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6nvr |
RMSD bond length | 0.006 |
RMSD bond angle | 1.045 |
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] | 86.590 | 86.590 | 1.630 |
High resolution limit [Å] | 1.550 | 4.890 | 1.550 |
Rmerge | 0.042 | 0.033 | 0.723 |
Rmeas | 0.045 | 0.036 | 0.772 |
Rpim | 0.016 | 0.013 | 0.270 |
Total number of observations | 578145 | ||
Number of reflections | 73287 | 2552 | 10650 |
<I/σ(I)> | 22.1 | ||
Completeness [%] | 99.4 | 99.9 | 100 |
Redundancy | 7.9 | 7.2 | 8 |
CC(1/2) | 0.999 | 0.999 | 0.838 |
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 |