6QOU
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 24 (Indole-6-boronic acid)
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | DIAMOND BEAMLINE I04-1 |
Synchrotron site | Diamond |
Beamline | I04-1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2015-12-14 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.9282 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 75.188, 79.070, 87.396 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 58.634 - 1.560 |
R-factor | 0.1846 |
Rwork | 0.183 |
R-free | 0.20600 |
Structure solution method | MOLECULAR REPLACEMENT |
RMSD bond length | 0.009 |
RMSD bond angle | 1.039 |
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] | 87.400 | 87.400 | 1.640 |
High resolution limit [Å] | 1.560 | 4.920 | 1.560 |
Rmerge | 0.030 | 0.016 | 0.825 |
Rmeas | 0.032 | 0.017 | 0.889 |
Rpim | 0.011 | 0.006 | 0.325 |
Total number of observations | 581731 | ||
Number of reflections | 75407 | 2607 | 10872 |
<I/σ(I)> | 30.6 | ||
Completeness [%] | 100.0 | 99.9 | 100 |
Redundancy | 7.7 | 7 | 7.3 |
CC(1/2) | 1.000 | 1.000 | 0.783 |
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 |