6YKO
Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Compound 11a
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | ESRF BEAMLINE MASSIF-3 |
Synchrotron site | ESRF |
Beamline | MASSIF-3 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2018-12-02 |
Detector | DECTRIS EIGER X 4M |
Wavelength(s) | 0.9677 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 49.536, 81.058, 225.181 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 76.267 - 2.210 |
R-factor | 0.1836 |
Rwork | 0.181 |
R-free | 0.23940 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6q89 |
Data reduction software | XDS |
Data scaling software | Aimless (0.7.2) |
Phasing software | PHASER |
Refinement software | PHENIX (1.15.2_3472) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 76.270 | 76.270 | 2.310 |
High resolution limit [Å] | 2.190 | 6.930 | 2.190 |
Rmerge | 0.083 | 0.028 | 0.850 |
Rmeas | 0.089 | 0.031 | 0.910 |
Rpim | 0.032 | 0.011 | 0.322 |
Total number of observations | 354104 | 11252 | 53895 |
Number of reflections | 47550 | 1700 | 6844 |
<I/σ(I)> | 15.4 | 44.5 | 2.3 |
Completeness [%] | 99.7 | 99.6 | 99.7 |
Redundancy | 7.4 | 6.6 | 7.9 |
CC(1/2) | 0.999 | 0.999 | 0.691 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 293 | Holo protein at 10 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 2.5 mM 2-mercaptoethanol was mixed with 0.1 M bis-tris propane pH 8.5, 0.1 M MgCl2, 20% w/v PEG 3350 and a crystal seed stock in a 0.75:1.0:0.25 (v/v) ratio. The seed stock was prepared in the same crystallization buffer. Suitable crystals were soaked with 2 mM synthesized compound 11a in an equilvalent precipitant solution supplemented with 22% v/v ethylene glycol. |