8PPG

Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with beta-D-glucopyranosyl 1,3,4,6-tetrakisphosphate/ADP/Mn after reaction

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	ESRF BEAMLINE ID23-1
Synchrotron site	ESRF
Beamline	ID23-1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2022-07-23
Detector	DECTRIS EIGER2 X CdTe 16M
Wavelength(s)	0.8856
Spacegroup name	C 2 2 21
Unit cell lengths	71.283, 97.102, 190.755
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	95.380 - 1.750
R-factor	0.20785
Rwork	0.206
R-free	0.24350
Structure solution method	FOURIER SYNTHESIS
RMSD bond length	0.008
RMSD bond angle	1.442
Data reduction software	XDS
Data scaling software	XDS
Phasing software	REFMAC
Refinement software	REFMAC (5.8.0258)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	190.760	1.780
High resolution limit [Å]	1.750	1.750
Rpim	0.024	0.572
Number of reflections	67053	3682
<I/σ(I)>	13.6	1.3
Completeness [%]	100.0	100
Redundancy	13.2	13.6
CC(1/2)	0.999	0.676

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291	0.81 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. Protein:precipitant ratio 1:1. Protein concentration: 17 mg/ml. Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. Soaking overnight with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 7 mM beta-D-glucopyranosyl 1,3,4-trisphosphate (substrate), 10 mM ATP and 10 mM MnCl2.