8PVP

Crystal structure of human Casein Kinase II subunit alpha (CK2a1) in complex with allosteric compound FGJG18


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2930.2 M ammonia sulphate 0.1 M bis-tris pH 5.5 23-26% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
3.1560.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.009α = 90
b = 127.009β = 90
c = 125.838γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-10-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA0.9999SLSX06DA

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
12.644.7499.30.99814.28.832045
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)
12.62.720.813

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 REPLACEMENTTHROUGHOUT2.644.7430374161499.120.223280.221610.25346RANDOM50.288
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]
0.850.85-1.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.469
r_dihedral_angle_2_deg9.215
r_scangle_other7.367
r_mcangle_other6.825
r_mcangle_it6.822
r_dihedral_angle_1_deg6.719
r_scbond_it5.048
r_scbond_other4.851
r_mcbond_it4.512
r_mcbond_other4.509
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.469
r_dihedral_angle_2_deg9.215
r_scangle_other7.367
r_mcangle_other6.825
r_mcangle_it6.822
r_dihedral_angle_1_deg6.719
r_scbond_it5.048
r_scbond_other4.851
r_mcbond_it4.512
r_mcbond_other4.509
r_angle_refined_deg1.52
r_angle_other_deg0.563
r_chiral_restr0.08
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 Atoms5336
Nucleic Acid Atoms
Solvent Atoms30
Heterogen Atoms133

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing