8S3D

Crystal structure of Medicago truncatula glutamate dehydrogenase 2 in complex with 2-amino-2-hydroxyglutarate (reaction intermediate) and NAD

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)	0.9762
Spacegroup name	P 21 21 21
Unit cell lengths	111.832, 155.707, 163.089
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	65.890 - 1.650
R-factor	0.1471
Rwork	0.147
R-free	0.17350
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.012
RMSD bond angle	1.153
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]	65.890	1.750
High resolution limit [Å]	1.650	1.650
Rmerge	0.092	1.445
Rmeas		1.548
Number of reflections	337626	53784
<I/σ(I)>	6.83	1.11
Completeness [%]	99.5	98.7
Redundancy	7.49	7.56
CC(1/2)	0.994	0.532

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.1M Amino acids (0.02M DL-Glutamic acid monohydrate; 0.02M DL-Alanine; 0.02M Glycine; 0.02M DL-Lysine monohydrochloride; 0.02M DL-Serine ) 0.1M Imidazole/MES monohydrate pH 6.5 20% v/v PEG 500* MME; 10 % w/v PEG 20000