9HYH | pdb_00009hyh

Protein kinase CK2 catalytic subunit alpha (CSNK2A1 gene product) in complex with F2X-Entry screen fragment D02 and CX-4945 (Silmitasertib)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PVR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Reservoir: 200 mM Li2SO4, 100 mM Bis-Tris/HCl, pH 6.5, 35 % PEG 3350 Protein/Ligand mix: 5 mg per mL CK2alpha1-335, 100 mM ligand, 0.5 mM CX-4945, 10 % DMSO, prequilibrated Drop: 4 microliter protein/ligand plus 2 microliter reservoir

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.172	α = 90
b = 127.172	β = 90
c = 124.93	γ = 90

Symmetry
Space Group	P 43 21 2

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 EIGER2 X 9M		2024-11-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.87313	ESRF	ID30B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1.96	72.984	100	0.34	0.067	0.997	8.9	26.3		73855			31.35

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.96	1.993			4.378	0.887	0.349	1.3

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	1.96	72.98	1.34	73468	1098	99.48	0.2011	0.2005	0.2008	0.241	0.2414	41.99

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	13.7065
f_angle_d	0.8016
f_chiral_restr	0.0525
f_plane_restr	0.008
f_bond_d	0.0063

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5597
Nucleic Acid Atoms
Solvent Atoms	406
Heterogen Atoms	82

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.