6YKK

Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Compound 15

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SOLEIL BEAMLINE PROXIMA 2
Synchrotron site	SOLEIL
Beamline	PROXIMA 2
Temperature [K]	100
Detector technology	PIXEL
Collection date	2019-09-27
Detector	DECTRIS EIGER X 9M
Wavelength(s)	0.980112
Spacegroup name	P 21 21 21
Unit cell lengths	49.165, 80.973, 224.022
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	112.011 - 2.236
R-factor	0.1915
Rwork	0.190
R-free	0.23080
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6q89
Data reduction software	XDS
Data scaling software	Aimless (0.7.4)
Phasing software	PHASER
Refinement software	PHENIX (1.15.2_3472)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	112.011	112.010	2.360
High resolution limit [Å]	2.236	7.070	2.240
Rmerge	0.207	0.084	1.448
Rmeas	0.221	0.090	1.539
Rpim	0.078	0.032	0.518
Total number of observations		11357	53728
Number of reflections	44350	1585	6359
<I/σ(I)>	8.5	19.9	2.2
Completeness [%]	100.0	99.8	100
Redundancy	7.9	7.2	8.4
CC(1/2)	0.994	0.994	0.683

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