9YIT

Crystal structure of glutamate dehydrogenase from Babesia microti in complex with NADP

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	NSLS-II BEAMLINE 19-ID
Synchrotron site	NSLS-II
Beamline	19-ID
Temperature [K]	100
Detector technology	PIXEL
Collection date	2025-05-25
Detector	DECTRIS EIGER2 XE 9M
Wavelength(s)	0.9786
Spacegroup name	P 1 21 1
Unit cell lengths	105.667, 125.313, 123.706
Unit cell angles	90.00, 100.29, 90.00

Refinement procedure

Resolution	48.020 - 2.280
R-factor	0.1919
Rwork	0.190
R-free	0.22350
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.004
RMSD bond angle	0.701
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX ((dev_5438: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	48.860	2.340
High resolution limit [Å]	2.280	2.280
Rmerge	0.177	1.332
Rmeas	0.191	1.442
Rpim	0.073	0.548
Total number of observations	994280	72665
Number of reflections	144200	10631
<I/σ(I)>	9.4	1.6
Completeness [%]	99.9
Redundancy	6.9	6.8
CC(1/2)	0.995	0.493

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	25% 3350, 0.1M Bis-Tris 6.5, 0.2M MgCl2. BamiA.17991.a.A21.PW39288 at 16.7 mg/mL. 2mM NADP added to the protein prior to crystallization. plate 19938 F4 drop1, Puck: PSL-0509, Cryo: 12.5% P200 + 87.5% crystallant.