6LPT

Crystal structure of human D-2-hydroxyglutarate dehydrogenase in complex with D-lactate (D-LAC)

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	72.263, 94.411, 73.575
Unit cell angles	90.00, 111.77, 90.00

Refinement procedure

Resolution	36.387 - 2.621
R-factor	0.1931
Rwork	0.191
R-free	0.23130
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	2.710
High resolution limit [Å]	2.620	5.640	2.620
Rmerge	0.154	0.060	0.656
Rmeas	0.166	0.065	0.708
Rpim	0.063	0.025	0.265
Total number of observations	188447
Number of reflections	27511	2801	2738
<I/σ(I)>	3
Completeness [%]	99.5	99.1	99.9
Redundancy	6.8	6.7	7
CC(1/2)		0.998	0.841

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