9R5B | pdb_00009r5b

Crystal structure of human protein kinase CK2 catalytic subunit (isoenzyme ck2alpha'; CSNK2A2 gene product) in complex with 6,7-dibromo-4,5-difluoro-1H-1,2,3-benzotriazole

X-RAY DIFFRACTION

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	8.5	293.15	180 MICROLITER ENZYME STOCK SOLUTION (6 MG/ML IN 500 MM NACL, 25 MM TRIS/HCL, PH 8.5) WERE MIXED and incubated WITH 20 MIKROLITER of a STOCK SOLUTION of the inhibitor 4B0 (10 MM 4B0 IN DMSO). 10 MICROLITERS OF the resulting solution WERE MIXED WITH 5 MICROLITERS OF RESERVOIR SOLUTION (900 MM LICL, 28 % (W/V) PEG 6000, 100 MM TRIS/HCL, PH 8.5) IN EACH WELL OF A CRYSTALLIZATION PLATE. A SINGLE MACROSEED, grown UNDER THE SAME CONDITIONS, WAS ADDED TO EACH DROPLET of the plate. THE DROPLETS WERE EQUILIBRATED AT 293.15 K using the sitting drop variant of the VAPOR DIFFUSION method. This procedure generated large single crystals of a CK2alpha'/4B0 complex. Afterwards, the inhibitor 4B0 was exchanged against 6,7-dibromo-4,5-difluoro-1H-1,2,3-benzotriazole by an extensive soaking procedure of several steps.

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.502	α = 112.764
b = 47.373	β = 90.005
c = 50.407	γ = 88.74

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 EIGER2 X 16M		2021-09-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.885603	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	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	1.008	46.464	72.7	0.061	0.061	0.074	0.041	0.992	11.7	3.3		151723			14

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.008	1.102			0.565	0.565	0.713	0.369	0.714	1.6

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	1.09	33.02	1.97	147879	7456	88.45	0.1523	0.1515	0.1663	0.1675	0.1774	20.73

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	13.9421
f_angle_d	1.2944
f_chiral_restr	0.0889
f_plane_restr	0.0144
f_bond_d	0.0112

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2759
Nucleic Acid Atoms
Solvent Atoms	378
Heterogen Atoms	26

Software

Software
Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

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.