6QO6
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 4 (5-Methoxybenzimidazole)
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | DIAMOND BEAMLINE I24 |
| Synchrotron site | Diamond |
| Beamline | I24 |
| Temperature [K] | 292 |
| 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 | 74.077, 78.772, 86.324 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 56.216 - 1.745 |
| R-factor | 0.1826 |
| Rwork | 0.181 |
| R-free | 0.20880 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 6nvr |
| RMSD bond length | 0.007 |
| RMSD bond angle | 1.008 |
| 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] | 78.770 | 78.770 | 1.840 |
| High resolution limit [Å] | 1.740 | 5.520 | 1.740 |
| Rmerge | 0.057 | 0.040 | 0.921 |
| Rmeas | 0.061 | 0.043 | 0.987 |
| Rpim | 0.022 | 0.016 | 0.353 |
| Total number of observations | 395496 | ||
| Number of reflections | 52140 | 1821 | 7493 |
| <I/σ(I)> | 18.8 | ||
| Completeness [%] | 100.0 | 99.8 | 100 |
| Redundancy | 7.6 | 6.6 | 7.8 |
| CC(1/2) | 0.999 | 0.998 | 0.750 |
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 |
