7VBU

Crystal structure of human pyruvate dehydrogenase kinase 2 in complex with compound 5

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SPRING-8 BEAMLINE BL41XU
Synchrotron site	SPring-8
Beamline	BL41XU
Temperature [K]	100
Detector technology	PIXEL
Collection date	2015-04-22
Detector	DECTRIS PILATUS3 S 6M
Wavelength(s)	1.0
Spacegroup name	P 64
Unit cell lengths	109.462, 109.462, 84.093
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	94.800 - 1.890
R-factor	0.1856
Rwork	0.185
R-free	0.19720
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	7ebh
RMSD bond length	0.002
RMSD bond angle	0.516
Data reduction software	DIALS
Data scaling software	Aimless
Phasing software	PHENIX (phenix.refine)
Refinement software	PHENIX (1.19.2_4158)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	94.800	1.940
High resolution limit [Å]	1.890	1.890
Rmerge	0.062	1.201
Rmeas	0.066	1.262
Rpim	0.020	0.387
Number of reflections	45254	3309
<I/σ(I)>	18.5	2.3
Completeness [%]	98.5	98.4
Redundancy	10.2	10.4
CC(1/2)	0.999	0.768

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	5.5	277.15	50 mM Na acetate pH 5.5, 100 mM magnesium chloride and 8% (v/v) isopropanol