9TFY | pdb_00009tfy

Arabidopsis thaliana Casein Kinase 2 (CK2) alpha1 - beta1 complex bound to inositol hexakisphosphate (InsP6)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	298	0.1 M Carboxylic acids (0.2 M sodium formate, 0.2 M ammonium acetate, 0.2 M sodium citrate tribasic dihy drate, 0.2 potassium sodium tartrate tetrahydrate, 0.2 M sodium oxamate), 0.1 M buffer system 2 (HEPES, MOPS, pH 7.2), 31% PrecipMix 2 (40% [v/v] Ethylene glycol, 20% [w/v] PEG 4,000, 20 % [w/v] PEG 3,350, 0.2 M sodium malonate, 0.1 M Bis-Tris [pH 6.5] (Morpheus G2, Molecular Dimensions)

Crystal Properties
Matthews coefficient	Solvent content
5.98	79.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 210.189	α = 90
b = 210.189	β = 90
c = 272.599	γ = 90

Symmetry
Space Group	I 41 2 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		2021-06-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.000040	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	5.5	40.07	99.8	0.267	0.998	13.01	26.6		10252		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	5.5	5.83	100		6.03	0.32	1.3	27.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5.5	40.07	10231	512	100	0.2487	0.2477	0.2386	0.2672	0.2714	RANDOM	300

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]
-6.8287			-6.8287		13.6574

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	19.46
t_omega_torsion	2.66
t_angle_deg	0.88
t_bond_d	0.007
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8642
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	74

Software

Software
Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing