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Monoclinic crystal 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 Protein: 5 mg per mL in 500 mM NaCl, 25 mM Tris-HCl, pH 8.5
Reservoir: 810 mM LiCl, 250 mM Tris-HCl, pH 8.5, 28 % PEG 6000
Drop: 3 microliter protein mixed with 3 microliter reservoir
Optimization by macroseeding and microseeding
Complex formation by soaking
Crystal Properties Matthews coefficient Solvent content 2.01 38.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.761 α = 90 b = 72.206 β = 91.912 c = 102.192 γ = 90
Symmetry Space Group P 1 21 1
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 4M 2025-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.96770 ESRF MASSIF-3
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 1.2 58.96 57.3 0.057 0.992 7.4 2.1 120002 10.45
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 1.204 1.372 0.458 0.619 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 1.2 58.96 1.36 119991 5955 57.32 0.1403 0.1384 0.1443 0.1782 0.1796 17.05
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 13.2476 f_angle_d 1.1032 f_chiral_restr 0.0904 f_plane_restr 0.0122 f_bond_d 0.0107
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5479 Nucleic Acid Atoms Solvent Atoms 567 Heterogen Atoms 41
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction STARANISO data scaling PHASER phasing