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Structure of protein kinase CK2 catalytic subunit CK2alpha' (CSNK2A2 gene product) in complex with the indenoindole-precursor compound JC0151
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HMQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 900 mM LiCl, 250 mM Tris-HCl pH 8.5, 28 % PEG 6000.
Protein (5 mg per mL in 500 mM NaCl, 25 mM Tris-HCl, pH 8.5) was preincubated with indenoindole-type inhibitor 4w at 0.5 mM. Drops were made in 2:1 ratio. Crystal growth was induced by microseeding and optimized by macroseeding
Crystal Properties Matthews coefficient Solvent content 2.39 48.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.274 α = 66.347 b = 47.833 β = 89.803 c = 50.581 γ = 89.064
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2025-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97624 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.097 46.27 7.5 0.058 0.995 7.5 2.8 80362 9.58
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 1.097 1.279 0.641 0.216 1.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.1 46.27 1.97 80086 3850 49.26 0.1579 0.1569 0.1634 0.1788 0.1845 16.79
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 14.1452 f_angle_d 1.1083 f_chiral_restr 0.0842 f_plane_restr 0.0119 f_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2759 Nucleic Acid Atoms Solvent Atoms 298 Heterogen Atoms 46
Software Software Software Name Purpose autoPROC data processing PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing STARANISO data scaling