9FBM | pdb_00009fbm

Structure of human protein kinase CK2 catalytic subunit (CK2alpha, CSNK2A1 gene product) in complex with the cyclic peptidomimetic compound 12 discovered by high-throughput screening

X-RAY DIFFRACTION

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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	7.5	293	protein solution: 97.5 mikroliter CK2alpha-1-335 solution (7 mg/ml in 500 mmol/l NaCl, 25 mmol/l Tris/HCl, pH 8.5) was mixed with 2.5 mikroliter 20 millimolar FMP37 in DMSO and incubated for 30 min. reservoir: 1.5 mol/l lithium sulphate, 100 mM sodium HEPES buffer, pH 7.5. crystallization drop: 4 microliter protein solution plus 2 microliter reservoir.

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.016	α = 90
b = 208.36	β = 90
c = 76.718	γ = 90

Symmetry
Space Group	P 21 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 EIGER X 4M		2023-10-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.9677	ESRF	MASSIF-3

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	2.054	76.718	87.5	0.562	0.562	0.57	0.095	0.994	9.6	35.3		68956			21.56

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	2.054	2.182	26.8		6.641	6.641	6.738	1.116	0.563	1.5	37.4

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	2.054	54.7	1.35	68935	1023	87.44	0.1855	0.1847	0.1845	0.2388	0.2385	32.82

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	12.9152
f_angle_d	0.8995
f_chiral_restr	0.0568
f_plane_restr	0.0077
f_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8387
Nucleic Acid Atoms
Solvent Atoms	765
Heterogen Atoms	226

Software

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