6LPQ

Crystal structure of human D-2-hydroxyglutarate dehydrogenase in complex with D-malate (D-MAL)

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	72.615, 94.569, 73.673
Unit cell angles	90.00, 111.55, 90.00

Refinement procedure

Resolution	41.136 - 2.800
R-factor	0.2167
Rwork	0.215
R-free	0.25490
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6lpn
RMSD bond length	0.003
RMSD bond angle	0.844
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	2.900
High resolution limit [Å]	2.800	6.030	2.800
Rmerge	0.297	0.112	0.801
Rmeas	0.326	0.122	0.892
Rpim	0.132	0.046	0.383
Total number of observations	132903
Number of reflections	21823	2329	1878
<I/σ(I)>	2.2
Completeness [%]	95.7	99.7	81.8
Redundancy	6.1	6.7	5.1
CC(1/2)		0.994	0.617

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