6YKS

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

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	49.023, 80.909, 224.177
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	65.603 - 1.970
R-factor	0.1766
Rwork	0.175
R-free	0.21660
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]	112.090	112.090	2.050
High resolution limit [Å]	1.950	6.160	1.950
Rmerge	0.074	0.028	0.859
Rmeas	0.079	0.030	0.921
Rpim	0.028	0.011	0.328
Total number of observations	533986	17344	72104
Number of reflections	66445	2343	9533
<I/σ(I)>	14.6	43.6	1.9
Completeness [%]	99.9	99.9	99.8
Redundancy	8	7.4	7.6
CC(1/2)	0.999	1.000	0.751

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