8BHD

N-terminal domain of Plasmodium berghei glutamyl-tRNA synthetase (Tbxo4 derivative crystal structure)

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	2020-06-11
Detector	DECTRIS EIGER X 16M
Wavelength(s)	1.631371
Spacegroup name	C 1 2 1
Unit cell lengths	130.110, 88.510, 168.640
Unit cell angles	90.00, 105.70, 90.00

Refinement procedure

Resolution	47.850 - 3.170
R-factor	0.1942
Rwork	0.192
R-free	0.23730
Structure solution method	SAD
RMSD bond length	0.003
RMSD bond angle	0.583
Data reduction software	XDS
Data scaling software	XSCALE
Phasing software	CRANK2
Refinement software	PHENIX (dev_4701)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	47.850	3.283
High resolution limit [Å]	3.170	3.170
Rmerge	0.123	2.335
Rmeas	0.126	2.395
Rpim	0.027	0.529
Number of reflections	61436	6200
<I/σ(I)>	14.87	1.13
Completeness [%]	99.8	99.47
Redundancy	21.2	19.8
CC(1/2)	1.000	0.789

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	Stock protein concentration: 6-9 mg/mL Well solution: 0.1 M HEPES-NaOH pH 7.5, 1.4-1.5 M ammonium sulfate, 10-20% (vol) glycerol Mix: 400 nL protein solution/seeds + 400 nL well solution Use of microseeding technique to improve crystal size. 1 microliter of a 100 mM Tbxo4 solution (ligand code 7MT) was added to the crystallization drop for a soacking of 1-2 minutes before freezing the crystals.