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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 low-salt conditions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NSZ
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: 24 % PEG3350, 0.2 M KCl;
DROP SOLUTION BEFORE EQULIBRATION: 0.5 MICROLITER PROTEIN/INHIBITOR COMPLEX SOLUTION + 0.5 MICROLITER RESERVOIR SOLUTION
Crystal Properties Matthews coefficient Solvent content 1.96 37.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.033 α = 90 b = 79.569 β = 90 c = 82.142 γ = 90
Symmetry Space Group P 21 21 21
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 1.519 41.5 100 0.05914 0.05914 0.999 15.82 4.1 49151 15.41
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 1.519 1.574 99 0.7874 0.661 1.89 4
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 3NSZ 1.519 41.464 1.35 49147 1031 99.74 0.1632 0.1628 0.1644 0.1826 0.1819
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 17.442 f_angle_d 1.29 f_chiral_restr 0.085 f_bond_d 0.014 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2788 Nucleic Acid Atoms Solvent Atoms 384 Heterogen Atoms 43
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing