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Crystal structure of human protein kinase CK2 catalytic subunit (isoenzyme ck2alpha'; CSNK2A2 gene product) in complex with 5,6-dibromo-4,7-difluoro-1H-1,2,3-benzotriazole
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 8.5 293.15 Reservoir: 900 mM LiCl, 100 mM TRIS-HCl pH 8.5, 28 % PEG6000
Protein/ligand mix: 5 mg per mL Ck2alpha Prime including 2 mM ligand and 10 % DMSO
Drop: 2:1 mix of protein/ligand vs reservoir
optimization: Micro- and Macroseeding
Crystal Properties Matthews coefficient Solvent content 2.4 48.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.367 α = 113.455 b = 47.779 β = 90.205 c = 50.57 γ = 90.621
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 2022-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.8731 ESRF ID30B
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 1.19 46.552 63.9 7.2 0.994 10.3 3.2 82712 14
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 1.19 1.313 1.096 0.374 2.2
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 1.19 32.93 1.99 81727 4095 64.59 0.128 0.1265 0.1403 0.1547 0.1621 17.2
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 12.897 f_angle_d 1.2563 f_chiral_restr 0.0999 f_plane_restr 0.0156 f_bond_d 0.0135
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2773 Nucleic Acid Atoms Solvent Atoms 444 Heterogen Atoms 25
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing