6YKN
Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Compound 11b
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 | 49.004, 81.749, 226.099 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 76.878 - 2.630 |
R-factor | 0.2003 |
Rwork | 0.198 |
R-free | 0.25380 |
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] | 76.880 | 76.880 | 2.770 |
High resolution limit [Å] | 2.627 | 8.310 | 2.630 |
Rmerge | 0.131 | 0.042 | 1.026 |
Rmeas | 0.139 | 0.045 | 1.084 |
Rpim | 0.045 | 0.015 | 0.346 |
Total number of observations | 8213 | 38420 | |
Number of reflections | 28093 | 1015 | 4006 |
<I/σ(I)> | 13 | 36.2 | 2.2 |
Completeness [%] | 100.0 | 99.4 | 100 |
Redundancy | 9.1 | 8.1 | 9.6 |
CC(1/2) | 0.997 | 0.998 | 0.710 |
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 11b in an equilvalent precipitant solution supplemented with 22% v/v ethylene glycol. |