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Complex structure of human protein kinase CK2 catalytic subunit with the inhibitor 4'-carboxy-6,8-chloro-flavonol (FLC21) crystallized under high-salt conditions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PVR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PROTEIN STOCK SOLUTION: 6 MG/ML
CK2ALPHA1-335 IN 0.5 M NACL, 25 MM TRIS/HCL, PH 8.5;
INHIBITOR STOCK SOLUTION: 10 MM INHIBITOR IN DMSO;
PROTEIN/INHIBITOR COMPLEX SOLUTION: 90 MICROLITER PROTEIN STOCK SOLUTION + 10 MICROLITER INHIBITOR STOCK SOLUTION;
RESERVOIR SOLUTION: 4.3 M
NACL, 0.1 M SODIUM CITRATE, PH 5.2;
DROP SOLUTION BEFORE EQULIBRATION: 0.5 MICROLITER PROTEIN/INHIBITOR COMPLEX SOLUTION + 0.5 MICROLITER RESERVOIR SOLUTION
Crystal Properties Matthews coefficient Solvent content 2.19 43.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.591 α = 90 b = 72.591 β = 90 c = 133.252 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 CCD MARMOSAIC 225 mm CCD 2012-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.218 49.1 100 0.1109 0.1109 0.999 0.1109 7.9 18350 36.83
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.218 2.297 100 1.169 0.616 1.84 7.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2PVR 2.218 49.085 1.36 18348 1034 99.95 0.1904 0.1881 0.1891 0.2283 0.2306
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 Key Refinement Restraint Deviation f_dihedral_angle_d 20.122 f_angle_d 0.465 f_chiral_restr 0.042 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2798 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 28
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing