6NW7
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with S-Adenosyl-L-homocysteine
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 | 2015-10-02 |
| Detector | DECTRIS PILATUS 6M-F |
| Wavelength(s) | 0.9282 |
| Spacegroup name | P 21 21 21 |
| Unit cell lengths | 75.334, 78.254, 88.005 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 58.479 - 1.481 |
| R-factor | 0.1791 |
| Rwork | 0.178 |
| R-free | 0.19450 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 6nvr |
| RMSD bond length | 0.008 |
| RMSD bond angle | 1.089 |
| 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] | 88.000 | 88.000 | 1.560 |
| High resolution limit [Å] | 1.480 | 4.680 | 1.480 |
| Rmerge | 0.032 | 0.022 | 0.720 |
| Rmeas | 0.035 | 0.023 | 0.772 |
| Rpim | 0.012 | 0.008 | 0.275 |
| Total number of observations | 672548 | ||
| Number of reflections | 87094 | 2974 | 12561 |
| <I/σ(I)> | 28.6 | ||
| Completeness [%] | 99.9 | 99.4 | 99.9 |
| Redundancy | 7.7 | 7 | 7.7 |
| CC(1/2) | 1.000 | 0.999 | 0.826 |
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 |
