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Protein kinase CK2 catalytic subunit alpha' (CSNK2A2 gene product) in complex with F2X-Entry screen fragment D04
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 Original reservoir: 900 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000
Protein mixture: 5 mg/mL CK2alpha Prime in 500 mM NaCl, 25 mM Tris HCl, pH 8.5, 1 mM CX-4945 and 5 % DMSO
Drop: 2 microliter reservoir, 4 microliter protein/CX-4945 mix
Crystal optimization by micro- and macroseeding
Ligand soaking: 100 mM ligand in 900 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000, 5 % DMSO
Equilibration for 24 h against new reservoir: 900 mM LiCl, 250 mM Tris HCl, pH 8.5, saturated PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.35 47.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.34 α = 113.51 b = 47.56 β = 89.76 c = 50.44 γ = 91.77
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 PILATUS3 S 6M 2024-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918400 BESSY 14.1
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 1.66 32.87 94.8 0.104 0.997 10.3 3.6 85746 20.09
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 1.66 1.719 1.484 0.336 0.9
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 1.66 32.87 1.95 44232 1321 94.75 0.1885 0.1874 0.1874 0.2228 0.2229 27.32
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 13.6875 f_angle_d 0.9559 f_chiral_restr 0.0606 f_bond_d 0.0102 f_plane_restr 0.0092
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2768 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 18
Software Software Software Name Purpose PHENIX refinement PHASER phasing XDS data reduction Aimless data scaling Coot model building