6LPX

Crystal structure of human D-2-hydroxyglutarate dehydrogenase in complex with 2-oxoglutarate (2-OG)

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SSRF BEAMLINE BL19U1
Synchrotron site	SSRF
Beamline	BL19U1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2019-04-29
Detector	PSI PILATUS 6M
Wavelength(s)	0.9788
Spacegroup name	P 1 21 1
Unit cell lengths	72.169, 94.940, 73.219
Unit cell angles	90.00, 112.30, 90.00

Refinement procedure

Resolution	36.265 - 2.800
R-factor	0.1897
Rwork	0.187
R-free	0.23550
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6lpn
Data reduction software	HKL-3000
Data scaling software	HKL-3000
Phasing software	PHENIX
Refinement software	PHENIX (1.14_3260)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	50.000	50.000	2.900
High resolution limit [Å]	2.792	6.030	2.800
Rmerge	0.284	0.084	1.094
Rmeas	0.309	0.091	1.197
Rpim	0.118	0.035	0.480
Number of reflections	22571	2310	2252
<I/σ(I)>	2.2
Completeness [%]	99.4	99.1	99.9
Redundancy	6.6	6.6	6
CC(1/2)		0.996	0.658

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	6.5	289	0.1M BIS-TRIS, pH 6.5, 25% (w/v) PEG 3350