7OSZ

Human Prolyl-tRNA Synthetase in Complex with L-proline and Compound 4d

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	ESRF BEAMLINE ID30B
Synchrotron site	ESRF
Beamline	ID30B
Temperature [K]	100
Detector technology	PIXEL
Collection date	2018-12-02
Detector	DECTRIS PILATUS3 6M
Wavelength(s)	0.976251
Spacegroup name	P 1 21 1
Unit cell lengths	69.671, 86.696, 83.117
Unit cell angles	90.00, 110.14, 90.00

Refinement procedure

Resolution	78.030 - 2.460
R-factor	0.223
Rwork	0.220
R-free	0.27770
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	5vad
Data reduction software	XDS
Data scaling software	Aimless (0.7.4)
Phasing software	PHASER
Refinement software	PHENIX (1.17.1_3660)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	78.030	78.030	2.590
High resolution limit [Å]	2.460	7.780	2.460
Rmerge	0.107	0.041	0.860
Rmeas	0.126	0.049	1.003
Rpim	0.065	0.026	0.509
Total number of observations	124080	3471	18757
Number of reflections	33733	1099	4920
<I/σ(I)>	7	18.4	1.5
Completeness [%]	99.6	98.4	99.8
Redundancy	3.7	3.2	3.8
CC(1/2)	0.996	0.997	0.727

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	MICROBATCH	7.5	293	The purified protein at 30 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 2.5 mM 2-mercaptoethanol was incubated with 10 mM L-proline, 2 mM compound and 12% (v/v) DMSO on ice for 1 hr. Crystals were grown in a Terasaki Microbatch plate by mixing 1 uL the pre-mix with 1 uL of reservoir solution containing 0.25-0.4 M SrCl2, 15-20% (v/v) PEG3350 and 100 mM HEPES pH 7.5. The drops were covered with paraffin oil. Crystals were flash frozen in liquid nitrogen directly from the plate.