9FBI | pdb_00009fbi

Structure of human protein kinase CK2 catalytic subunit (CK2alpha', CSNK2A2 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	6HMQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	protein solution: 90 mikroliter CK2alpha'-Cys336Ser solution (5 mg/ml in 500 mmol/l NaCl, 25 mmol/l Tris/HCl, pH 8.5) was mixed with 10 mikroliter 10 millimolar FMP37 in DMSO and incubated for 30 min. reservoir: 810 mmol/l LiCl, 100 mM Tris/HCl, pH 8.5, 28%(w/v) PEG6000. crystallization drop: 4 mikroliter protein solution plus 2 mikroliter reservoir solution.

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.452	α = 90
b = 71.068	β = 91.967
c = 102.878	γ = 90

Symmetry
Space Group	P 1 21 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 S 9M		2022-11-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.885602	ESRF	ID30B

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	1.161	58.462	52	0.081	0.081	0.096	0.04	0.906	7.2	4.9		119426			13.04

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	1.161	1.329			1.275	1.275	1.436	0.77	0.535	1.8

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	1.161	58.46	1.35	119368	1205	51.94	0.1456	0.1452	0.1524	0.1847	0.1881	20.49

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	14.8404
f_angle_d	1.4279
f_chiral_restr	0.1042
f_bond_d	0.0181
f_plane_restr	0.0151

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5528
Nucleic Acid Atoms
Solvent Atoms	469
Heterogen Atoms	117

Software

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