6YKV

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

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SOLEIL BEAMLINE PROXIMA 1
Synchrotron site	SOLEIL
Beamline	PROXIMA 1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2019-02-15
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.978566
Spacegroup name	P 21 21 21
Unit cell lengths	49.109, 80.729, 224.377
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	56.094 - 2.430
R-factor	0.1925
Rwork	0.190
R-free	0.24170
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]	112.190	112.190	2.480
High resolution limit [Å]	2.360	7.450	2.360
Rmerge	0.123	0.045	1.240
Rmeas	0.129	0.048	1.307
Rpim	0.040	0.015	0.408
Total number of observations	379192	12188	54010
Number of reflections	37908	1369	5437
<I/σ(I)>	11.7	34.4	1.9
Completeness [%]	100.0	99.8	100
Redundancy	10	8.9	9.9
CC(1/2)	0.998	0.999	0.671

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