6LPP

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

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	2019-03-31
Detector	PSI PILATUS 6M
Wavelength(s)	0.9789
Spacegroup name	P 1 21 1
Unit cell lengths	72.275, 94.593, 73.399
Unit cell angles	90.00, 111.90, 90.00

Refinement procedure

Resolution	40.781 - 2.650
R-factor	0.2055
Rwork	0.203
R-free	0.24590
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	2.740
High resolution limit [Å]	2.639	5.710	2.650
Rmerge	0.104	0.050	0.375
Rmeas	0.123	0.059	0.451
Rpim	0.065	0.032	0.247
Number of reflections	26662	2717	2622
<I/σ(I)>	4
Completeness [%]	99.0	98.7	98.1
Redundancy	3.4	3.4	3.2
CC(1/2)		0.996	0.852

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