9QB9

CK2, catalytic subunit alpha' (CSNK2A2 gene product) in complex with a heparin-derived trisaccharide and the ATP-competitive inhibitor 4w

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	2024-05-12
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.976260
Spacegroup name	P 1
Unit cell lengths	46.537, 47.648, 50.438
Unit cell angles	66.53, 89.38, 87.97

Refinement procedure

Resolution	43.680 - 1.190
R-factor	0.1437
Rwork	0.143
R-free	0.17480
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.005
RMSD bond angle	0.875
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX (1.21.2_5419)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	46.505	1.410
High resolution limit [Å]	1.190	1.190
Rmerge	0.054	0.822
Number of reflections	67406	3370
<I/σ(I)>	4.2	1.5
Completeness [%]	52.5
Redundancy	2.3
CC(1/2)	0.996	0.318

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		293	Original reservoir: 900 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000 Protein mixture: 5 mg/mL CK2alpha Prime in 500 mM NaCl, 25 mM Tris HCl, pH 8.5, 1 mM 4w and 10 % DMSO Drop: 2 microliter reservoir, 4 microliter protein/4w mix Crystal optimization by micro- and macroseeding Desalting process: Step-wise replacement of original drop solution by 50 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000, 5 % DMSO over 10 days Ligand soaking: 100 mM ligand in 50 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000, 5 % DMSO Equilibration for 24 h against new reservoir: 50 mM LiCl, 250 mM Tris HCl, pH 8.5, saturated PEG 6000