6QOD
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 7 (2-Amino-6-fluorobenzothiazole)
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 | 74.143, 78.379, 86.540 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 56.305 - 1.852 |
R-factor | 0.1858 |
Rwork | 0.184 |
R-free | 0.21160 |
Structure solution method | MOLECULAR REPLACEMENT |
RMSD bond length | 0.007 |
RMSD bond angle | 1.014 |
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] | 86.540 | 86.540 | 1.950 |
High resolution limit [Å] | 1.850 | 5.860 | 1.850 |
Rmerge | 0.080 | 0.043 | 0.974 |
Rmeas | 0.086 | 0.046 | 1.046 |
Rpim | 0.031 | 0.018 | 0.378 |
Total number of observations | 329136 | ||
Number of reflections | 43636 | 1537 | 6276 |
<I/σ(I)> | 15.8 | ||
Completeness [%] | 99.9 | 99.8 | 99.9 |
Redundancy | 7.5 | 6.5 | 7.6 |
CC(1/2) | 0.999 | 0.998 | 0.702 |
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 |