9EQ1

Crystal structure of human Casein Kinase II subunit alpha (CK2a1) in complex with allosteric ligand FGJM24


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52930.1 M bis-tris pH 5.5 23-26% (v/v) PEG 3350 0.2 M ammonia sulphate
Crystal Properties
Matthews coefficientSolvent content
3.1360.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.743α = 90
b = 126.743β = 90
c = 125.725γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2024-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97625DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
13126.741000.9979.127.221155
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
133.180.803

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT389.622012597699.990.211510.209610.25067RANDOM62.906
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]
2.392.39-4.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.82
r_dihedral_angle_2_deg14.175
r_long_range_B_other11.565
r_long_range_B_refined11.559
r_scangle_other8.216
r_dihedral_angle_1_deg7.317
r_mcangle_it5.939
r_mcangle_other5.939
r_scbond_it5.247
r_scbond_other5.247
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.82
r_dihedral_angle_2_deg14.175
r_long_range_B_other11.565
r_long_range_B_refined11.559
r_scangle_other8.216
r_dihedral_angle_1_deg7.317
r_mcangle_it5.939
r_mcangle_other5.939
r_scbond_it5.247
r_scbond_other5.247
r_mcbond_it3.73
r_mcbond_other3.73
r_angle_refined_deg1.502
r_angle_other_deg0.524
r_chiral_restr0.068
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5459
Nucleic Acid Atoms
Solvent Atoms10
Heterogen Atoms179

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing