8PVO

Crystal structure of human Casein Kinase II subunit alpha (CK2a1) in complex with allosteric compound FG5


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6Z83 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.52930.2 M ammonia sulphate 0.1 M bis-tris pH 5.5 23-26% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
3.1360.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.648α = 90
b = 127.648β = 90
c = 123.901γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2023-03-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.99999SLSX06SA

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
12.2545.171000.99916.913.449160
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)
12.252.320.7781.8

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 REPLACEMENTTHROUGHOUT2.2545.1746690239999.970.20980.207640.25252RANDOM53.18
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]
2.112.11-4.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.454
r_dihedral_angle_2_deg13.539
r_scangle_other7.731
r_dihedral_angle_1_deg6.382
r_mcangle_it5.84
r_mcangle_other5.84
r_scbond_it5.773
r_scbond_other5.515
r_mcbond_it4.335
r_mcbond_other4.334
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.454
r_dihedral_angle_2_deg13.539
r_scangle_other7.731
r_dihedral_angle_1_deg6.382
r_mcangle_it5.84
r_mcangle_other5.84
r_scbond_it5.773
r_scbond_other5.515
r_mcbond_it4.335
r_mcbond_other4.334
r_angle_refined_deg1.52
r_angle_other_deg0.574
r_chiral_restr0.086
r_bond_refined_d0.008
r_gen_planes_refined0.008
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 Atoms5500
Nucleic Acid Atoms
Solvent Atoms148
Heterogen Atoms193

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing