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Structure of protein kinase CK2alpha in complex with AMPPNP crystallized in space group P43212
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, 25 % PEG3350
Protein: 5 mg/mL in 500 mM NaCl, 25 mM Tris/HCl, pH 8.5
Drop: 2 to ratio of protein to reservoir
Soaking with AMPPNO and MgCl2
Crystal Properties Matthews coefficient Solvent content 2.68 54.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.019 α = 90 b = 128.019 β = 90 c = 124.164 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 EIGER X 16M 2024-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.96770 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 1.86 89.129 69.4 0.364 0.993 7.6 19.3 60043 19.74
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 1.86 2.081 3.154 0.696 1.7
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 1.86 73.15 1.34 60011 2930 69.36 0.177 0.1747 0.1753 0.2215 0.2217 27.61
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 15.3705 f_angle_d 1.2284 f_chiral_restr 0.0754 f_bond_d 0.0132 f_plane_restr 0.0123
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5572 Nucleic Acid Atoms Solvent Atoms 541 Heterogen Atoms 116
Software Software Software Name Purpose autoPROC data processing PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing STARANISO data scaling