6QOM
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 16 (2-Amino-3-nitropyridine)
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | DIAMOND BEAMLINE I24 |
| Synchrotron site | Diamond |
| Beamline | I24 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2015-11-23 |
| Detector | DECTRIS PILATUS 6M |
| Wavelength(s) | 0.9686 |
| Spacegroup name | P 21 21 21 |
| Unit cell lengths | 73.955, 79.592, 85.853 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 54.177 - 1.900 |
| R-factor | 0.1944 |
| Rwork | 0.192 |
| R-free | 0.22960 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.007 |
| RMSD bond angle | 1.068 |
| Data reduction software | XDS |
| Data scaling software | Aimless (0.5.15) |
| Phasing software | PHASER (2.5.7) |
| Refinement software | PHENIX (1.9_1692) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 79.590 | 79.590 | 2.000 |
| High resolution limit [Å] | 1.900 | 6.000 | 1.900 |
| Rmerge | 0.060 | 0.041 | 0.890 |
| Rmeas | 0.065 | 0.044 | 0.954 |
| Rpim | 0.023 | 0.016 | 0.341 |
| Total number of observations | 9451 | 45315 | |
| Number of reflections | 40803 | 1434 | 5867 |
| <I/σ(I)> | 16.9 | 36.7 | 2.6 |
| Completeness [%] | 99.9 | 99.7 | 100 |
| Redundancy | 7.6 | 6.6 | 7.7 |
| CC(1/2) | 0.999 | 0.999 | 0.797 |
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 |
