6LPU

Crystal structure of human D-2-hydroxyglutarate dehydrogenase in complex with L-2-hydroxyglutarate (L-2-HG)

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SSRF BEAMLINE BL17U1
Synchrotron site	SSRF
Beamline	BL17U1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2019-05-10
Detector	DECTRIS PILATUS 6M
Wavelength(s)	0.9792
Spacegroup name	P 1 21 1
Unit cell lengths	71.709, 94.530, 72.789
Unit cell angles	90.00, 112.25, 90.00

Refinement procedure

Resolution	47.265 - 2.923
R-factor	0.2256
Rwork	0.224
R-free	0.25500
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6lpn
RMSD bond length	0.004
RMSD bond angle	0.986
Data reduction software	HKL-3000
Data scaling software	HKL-3000
Phasing software	PHENIX
Refinement software	PHENIX (1.15rc1_3420)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	50.000	50.000	3.110
High resolution limit [Å]	2.923	6.460	3.000
Rmerge	0.220	0.079	0.742
Rmeas	0.250	0.091	0.843
Rpim	0.115	0.043	0.389
Number of reflections	19104	1966	1877
<I/σ(I)>	3.9
Completeness [%]	99.5	99.3	97.8
Redundancy	4.8	4.7	4.4
CC(1/2)		0.989	0.651

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