6WBD
Crystal Structure of Lysyl-tRNA synthetase from Stenotrophomonas maltophilia with bound L-lysine
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 | 2020-02-13 |
Detector | RAYONIX MX-300 |
Wavelength(s) | 0.97872 |
Spacegroup name | P 31 2 1 |
Unit cell lengths | 127.160, 127.160, 158.700 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 41.620 - 2.050 |
R-factor | 0.1514 |
Rwork | 0.149 |
R-free | 0.18390 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 1bbu |
RMSD bond length | 0.007 |
RMSD bond angle | 0.805 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | MoRDa |
Refinement software | PHENIX (1.17.1-3360) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 50.000 | 2.100 |
High resolution limit [Å] | 2.050 | 9.170 | 2.050 |
Rmerge | 0.080 | 0.032 | 0.560 |
Rmeas | 0.085 | 0.035 | 0.600 |
Number of reflections | 87130 | 978 | 6522 |
<I/σ(I)> | 17.32 | 49.58 | 3.4 |
Completeness [%] | 93.3 | 83.4 | 95.6 |
Redundancy | 8.035 | 7.668 | 7.897 |
CC(1/2) | 0.999 | 0.999 | 0.878 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 287 | StmaA.00612.a.B1.PW38745 at 10 mg/ml was incubated with 2 mM L-lysine and adenosine, then mixed 1:1 with Morpheus(H6): 10% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 0.1 M MOPS/HEPES-Na pH 7.5, 0.02 M each sodium L-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine. Tray 313975h6. Puck xdi4-1. |