8OWM

Crystal structure of glutamate dehydrogenase 2 from Arabidopsis thaliana binding Ca, NAD and 2,2-dihydroxyglutarate

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)
Synchrotron site	PETRA III, EMBL c/o DESY
Beamline	P13 (MX1)
Temperature [K]	100
Detector technology	PIXEL
Collection date	2021-06-21
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.976200
Spacegroup name	P 1
Unit cell lengths	95.544, 95.629, 95.841
Unit cell angles	90.42, 93.59, 117.78

Refinement procedure

Resolution	65.700 - 1.700
R-factor	0.1441
Rwork	0.144
R-free	0.17210
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6yei
RMSD bond length	0.009
RMSD bond angle	0.995
Data reduction software	XDS
Data scaling software	XSCALE
Phasing software	PHASER
Refinement software	PHENIX (1.18.1_3865)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	65.700	1.800
High resolution limit [Å]	1.700	1.700
Rmerge	0.062	0.758
Rmeas	0.075	0.927
Number of reflections	318817	50659
<I/σ(I)>	10.76	1.32
Completeness [%]	96.9	95.2
Redundancy	3.55	2.92
CC(1/2)	0.998	0.624

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	6.5	273	0.12MMonosaccharides (0.02M D-Glucose; 0.02M D-Mannose; 0.02M D-Galactose; 0.02M L-Fucose; 0.02M D-Xylose; 0.02M N-Acetyl-D-Glucosamine ),0.1M Imidazole/MES buffer pH 6.5, 20% v/v Glycerol and 10% w/v PEG 4000