5VL1

Crystal Structure of Lysyl-tRNA Synthetase from Mycobacterium ulcerans complexed with L-lysine

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	APS BEAMLINE 21-ID-F
Synchrotron site	APS
Beamline	21-ID-F
Temperature [K]	100
Detector technology	CCD
Collection date	2017-04-12
Detector	MARMOSAIC 300 mm CCD
Wavelength(s)	0.97872
Spacegroup name	P 1
Unit cell lengths	95.040, 96.690, 105.560
Unit cell angles	90.38, 104.84, 117.15

Refinement procedure

Resolution	46.455 - 2.700
R-factor	0.1777
Rwork	0.177
R-free	0.20430
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	3a74
RMSD bond length	0.002
RMSD bond angle	0.500
Data reduction software	XDS
Data scaling software	XSCALE
Phasing software	MoRDa
Refinement software	PHENIX

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	46.455	46.455	2.770
High resolution limit [Å]	2.700	12.070	2.700
Rmerge	0.082	0.036	0.599
Rmeas	0.096	0.042	0.692
Total number of observations	342637
Number of reflections	86858	958	6396
<I/σ(I)>	12.14	29.34	2.36
Completeness [%]	98.8	97.8	98.2
Redundancy	3.945	3.694	3.986
CC(1/2)	0.997	0.998	0.805

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		290	MyulA.00612.a.B1.PW37993 at 28 mg/ml was incubated with 3 mM MgCl2, AMPPNP, and L-Lysine, then mixed 1:1 with Morpheus(e9): 10% (w/v) PEG-20,000, 20% (v/v) PEG MME 550, 0.1 M bicine/ Trisma base, pH = 8.5, and 0.03 M each diethyleneglycol, triethyleneglycol, tetraethyleneglycol, pentaethylene glycol