5OMY

HIGH-SALT STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA) IN COMPLEX WITH THE INDENOINDOLE-TYPE INHIBITOR 4P

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		293.15	90 MIKROLITER ENZYME STOCK SOLUTION (6 MG/ML IN 500 MM NACL, 25 MM TRIS/HCL, PH 8.5) WAS MIXED WITH 10 MIKROLITER 4P STOCK SOLUTION (10 MM 4P IN DMSO). THIS MIXTURE WAS INCUBATED FOR 30 MIN AT ROOM TEMPERATURE. THE RESERVOIR SOLUTION OF THE CRYSTALLIZATION EXPERIMENT WAS 4.2 M NACL, 0.1 M CITRIC ACID, PH 5.5. PRIOR TO EQUILIBRATION THE CRYSTALLIZATION DROP WAS COMPOSED OF 1 MIKROLITER RESERVOIR SOLUTION PLUS 1 MIKROLITER ENZYME/4P MIXTURE., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.698	α = 90
b = 72.698	β = 90
c = 132.887	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 PILATUS 2M-F		2017-02-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.97625	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.95	63.78	99.94	0.09151	20.77	24.9		26747			43.54

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	1.95	2.02	100		2.281	0.64	1.52	26.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2PVR	1.95	63.778	1.33	26733	1316	99.94	0.1939	0.1925	0.2208

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	11.791
f_angle_d	0.57
f_chiral_restr	0.045
f_plane_restr	0.004
f_bond_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2804
Nucleic Acid Atoms
Solvent Atoms	122
Heterogen Atoms	32

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	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.