9QB9 | pdb_00009qb9

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6HMQ

Crystallization

Crystalization Experiments
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

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.537	α = 66.528
b = 47.648	β = 89.377
c = 50.438	γ = 87.971

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M		2024-05-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.976260	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.19	46.505	52.5	0.054	0.996	4.2	2.3		67406			11.95

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.19	1.41			0.822	0.318	1.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.19	43.68	1.96	63209	1230	49.98	0.1437	0.1431	0.1504	0.1748	0.1792	20.53

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.9983
f_angle_d	0.8754
f_chiral_restr	0.0676
f_plane_restr	0.0083
f_bond_d	0.0047

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2759
Nucleic Acid Atoms
Solvent Atoms	232
Heterogen Atoms	79

Software

Software
Software Name	Purpose
PHENIX	refinement
PHASER	phasing
XDS	data reduction
Aimless	data scaling
autoPROC	data processing