5BYB

Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with ADP and 1,5-(PA)2-IP4

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	APS BEAMLINE 22-BM
Synchrotron site	APS
Beamline	22-BM
Temperature [K]	100
Detector technology	CCD
Collection date	2015-04-10
Detector	MARMOSAIC 225 mm CCD
Wavelength(s)	1.0
Spacegroup name	P 21 21 21
Unit cell lengths	88.807, 110.411, 41.423
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	35.570 - 2.300
R-factor	0.19287
Rwork	0.189
R-free	0.24638
Structure solution method	FOURIER SYNTHESIS
Starting model (for MR)	3t7a
RMSD bond length	0.011
RMSD bond angle	1.738
Data scaling software	HKL-2000
Phasing software	PHASER
Refinement software	REFMAC (5.7.0032)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	50.000	50.000	2.340
High resolution limit [Å]	2.300	6.240	2.300
Rmerge		0.030	0.438
Rmeas	0.128	0.034	0.490
Rpim	0.057	0.015	0.215
Total number of observations	88600
Number of reflections	18773
<I/σ(I)>	6
Completeness [%]	99.2	99	95.5
Redundancy	4.7	4.3	4.7
CC(1/2)		0.999	0.890

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	7	277	12% (w/v) PEG 3350, 20 mM MgCl2, 0.1 M HEPES, pH 7.0, 1 mM ATP and 2 mM CdCl2. The crystals were transferred to a stabilizing buffer containing 22% (w/v) PEG 3350, 10 mM MgCl2, 0.1 M sodium acetate, pH 5.2 at 4 oC overnight, while ATP in the crystals was hydrolyzed to ADP. The crystals were soaked under the above stabilizing buffer for three days with 2 mM analog.