9GXY

Crystal structure of protein kinase CK2 catalytic subunit (CSNK2A2 gene product) in complex with the dual CK2/HDAC inhibitor IOR-160

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)
Synchrotron site	PETRA III, EMBL c/o DESY
Beamline	P13 (MX1)
Temperature [K]	100
Detector technology	PIXEL
Collection date	2024-09-16
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.9763
Spacegroup name	P 1
Unit cell lengths	46.343, 47.734, 50.706
Unit cell angles	66.58, 89.78, 88.99

Refinement procedure

Resolution	41.060 - 1.160
R-factor	0.1606
Rwork	0.160
R-free	0.17780
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.012
RMSD bond angle	1.274
Data reduction software	autoPROC
Data scaling software	autoPROC
Phasing software	PHASER
Refinement software	PHENIX (1.20.1-4487)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	46.529	1.202
High resolution limit [Å]	1.157	1.161
Rmerge	0.073	2.182
Rmeas	0.078
Rpim	0.028
Number of reflections	84256	426
<I/σ(I)>	16	1.6
Completeness [%]	59.8
Redundancy	7.5
CC(1/2)	0.997	0.694

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	Original crystal: 47.5 microliter CK2alphaPrime mixed with 2.5 microliter of a 20 mM CX-4945 solution in DMSO to a final concentration of 5 mg per mL protein and 1 mM CX-4945. Reservoir (900 mM LiCl, 250 mM TRIS HCl, pH 8.5, 28 % PEG 6000) was mixed 1:2 with protein stock. Crystal were optimized by micro- and macroseeding. IOR-160 was introduced by back-soaking: 8 microliter reservoir were mixed for this with with 2 microliter of a 10 mM IOR-160 stock in DMSO. The crystal was soaked in 4 microliters of this solution of 72 hours.