6Z83

CK2 alpha bound to chemical probe SGC-CK2-1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6YUL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2 M ammonia sulphate 0.1 M bis-tris pH 5.5 23-26% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.93	58.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.96	α = 90
b = 126.96	β = 90
c = 124.6	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		2020-05-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.99999	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.17	44.89	100	0.999	16.3	26.5		54337

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.17	2.23			0.761

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6yul	2.171	44.89	54265	2767	99.956	0.216	0.214	0.2446	36.336

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]
1.648			1.648		-3.296

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.756
r_dihedral_angle_4_deg	17.312
r_dihedral_angle_3_deg	15.056
r_dihedral_angle_1_deg	6.276
r_lrange_it	5.088
r_lrange_other	5.088
r_scangle_it	2.69
r_scangle_other	2.689
r_mcangle_it	2.452
r_mcangle_other	2.452
r_scbond_it	1.593
r_scbond_other	1.593
r_angle_other_deg	1.495
r_mcbond_other	1.476
r_mcbond_it	1.475
r_angle_refined_deg	1.42
r_nbd_refined	0.215
r_nbd_other	0.209
r_symmetry_xyhbond_nbd_refined	0.2
r_nbtor_refined	0.18
r_symmetry_nbd_other	0.179
r_symmetry_nbd_refined	0.143
r_xyhbond_nbd_refined	0.12
r_chiral_restr	0.089
r_symmetry_nbtor_other	0.081
r_ext_dist_refined_d	0.044
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5441
Nucleic Acid Atoms
Solvent Atoms	275
Heterogen Atoms	165

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing