6AQH
Crystal Structure of Lysyl-tRNA Synthetase from Mycobacterium thermoresistibile complexed with L-lysine and Cladosporin
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 21-ID-F |
Synchrotron site | APS |
Beamline | 21-ID-F |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2017-08-04 |
Detector | MARMOSAIC 300 mm CCD |
Wavelength(s) | 0.97872 |
Spacegroup name | P 1 |
Unit cell lengths | 53.460, 88.160, 123.430 |
Unit cell angles | 93.34, 96.45, 98.93 |
Refinement procedure
Resolution | 42.457 - 2.350 |
R-factor | 0.225 |
Rwork | 0.224 |
R-free | 0.25380 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5vl1 |
RMSD bond length | 0.002 |
RMSD bond angle | 0.437 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | PHASER |
Refinement software | PHENIX |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 42.457 | 42.457 | 2.410 |
High resolution limit [Å] | 2.350 | 10.510 | 2.350 |
Rmerge | 0.054 | 0.029 | 0.576 |
Rmeas | 0.072 | 0.037 | 0.751 |
Total number of observations | 199158 | ||
Number of reflections | 87176 | 970 | 6521 |
<I/σ(I)> | 10.13 | 22.91 | 1.97 |
Completeness [%] | 94.8 | 94.6 | 95.5 |
Redundancy | 2.285 | 2.225 | 2.378 |
CC(1/2) | 0.997 | 0.997 | 0.866 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 9.1 | 290 | MythA.00612.a.B1.PW38257 at 33.5 mg/ml was incubated with 2 mM L-Lysine and 1 mM cladosporin, then mixed 1:1 with MCSG1 (d12): 0.2 M ammonium chloride, pH = 6.3, 20% (w/v) PEG-3350, cryoprotected with 20% ethylene glycol. Tray: 293203d12, puck: ryc9-9. |