6YKQ

Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Compound 11c

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	49.243, 80.796, 222.916
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	55.729 - 1.940
R-factor	0.1727
Rwork	0.172
R-free	0.20870
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]	80.800	80.800	2.000
High resolution limit [Å]	1.900	6.010	1.900
Rmerge	0.102	0.044	0.972
Rmeas	0.110	0.048	1.041
Rpim	0.040	0.017	0.368
Total number of observations	526716	16920	80280
Number of reflections	70693	2495	10166
<I/σ(I)>	12.5	33.1	2.1
Completeness [%]	99.4	99.6	99.9
Redundancy	7.5	6.8	7.9
CC(1/2)	0.998	0.998	0.703

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 11c in an equilvalent precipitant solution supplemented with 22% v/v ethylene glycol.