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Protein kinase CK2 catalytic subunit alpha (CSNK2A1 gene product) in complex with F2X-Entry screen fragment D02 and CX-4945 (Silmitasertib)
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 Reservoir: 200 mM Li2SO4, 100 mM Bis-Tris/HCl, pH 6.5, 35 % PEG 3350
Protein/Ligand mix: 5 mg per mL CK2alpha1-335, 100 mM ligand, 0.5 mM CX-4945, 10 % DMSO, prequilibrated
Drop: 4 microliter protein/ligand plus 2 microliter reservoir
Crystal Properties Matthews coefficient Solvent content 2.99 58.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.172 α = 90 b = 127.172 β = 90 c = 124.93 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 PIXEL DECTRIS EIGER2 X 9M 2024-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.87313 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.96 72.984 100 0.34 0.067 0.997 8.9 26.3 73855 31.35
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.96 1.993 4.378 0.887 0.349 1.3
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 1.96 72.98 1.34 73468 1098 99.48 0.2011 0.2005 0.2008 0.241 0.2414 41.99
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 13.7065 f_angle_d 0.8016 f_chiral_restr 0.0525 f_plane_restr 0.008 f_bond_d 0.0063
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5597 Nucleic Acid Atoms Solvent Atoms 406 Heterogen Atoms 82
Software Software Software Name Purpose PHENIX refinement PHASER phasing XDS data reduction Aimless data scaling autoPROC data processing