5OOI

STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA') IN COMPLEX WITH THE INDENOINDOLE-TYPE INHIBITOR 4P


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3OFM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29390 MIKROLITER ENZYME STOCK SOLUTION (5 MG/ML IN 500 MM NACL, 25 MM TRIS/HCL, PH 8.5) WAS MIXED WITH 10 MIKROLITER 4P STOCK SOLUTION (10 MM 4P IN DMSO). THIS MIXTURE WAS INCUBATED FOR 30 MIN AT ROOM TEMPERATURE. THE RESERVOIR SOLUTION OF THE CRYSTALLIZATION EXPERIMENT WAS 25 % (W/ V) PEG3350, 0.2 M AMMONIUM ACETATE, 0.1 M HEPES BUFFER, PH 8.5. PRIOR TO EQUILIBRATION THE CRYSTALLIZATION DROP WAS COMPOSED OF 1 MIKROLITER RESERVOIR SOLUTION PLUS 1 MIKROLITER ENZYME/4P MIXTURE., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
Crystal Properties
Matthews coefficientSolvent content
2.448.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.488α = 90
b = 112.128β = 90
c = 143.692γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2017-07-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)1.0000PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (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
11.99871.4899.690.1770.1770.9997.396.75174224.98
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9982.0797.591.1911.1910.6731.416.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3OFM1.99871.4851726104199.70.17480.17380.2211
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.522
f_angle_d1.124
f_chiral_restr0.067
f_bond_d0.011
f_plane_restr0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5513
Nucleic Acid Atoms
Solvent Atoms443
Heterogen Atoms83

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing