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Structure of protein kinase ck2 catalytic subunit (csnk2a1 gene product) in complex with the bivalent inhibitor KN2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6TEI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 reservoir composition: 30 % (w/v) PEG8000, 0.2 M ammonium sulfate, 0.1 M sodium cacodylate, pH 6.5; crystallization drop composition before equilibration: 0.01 ml reservoir solution plus 0.02 ml enzyme stock solution (6 mg/ml enzyme, 0.5 M NaCl, 25 mM Tris/HCl, pH 8.5); the bivalent inhibitor KN2 was introduced by extensive soaking
Crystal Properties Matthews coefficient Solvent content 3.19 61.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.591 α = 90 b = 127.591 β = 90 c = 124.52 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 PILATUS 6M 2019-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.920200 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) 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 1.763 89.115 74 0.111 0.111 0.113 0.022 0.998 20.4 26.5 74986 29.81
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.763 1.921 16.4 2.229 2.229 2.27 0.428 0.697 27.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6TEI 1.77 73.06 1.33 74959 1476 74.91 0.1743 0.1739 0.1745 0.1947 0.1939 40.29
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 21.6825 f_angle_d 0.7129 f_chiral_restr 0.05 f_bond_d 0.0047 f_plane_restr 0.0045
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5597 Nucleic Acid Atoms Solvent Atoms 419 Heterogen Atoms 124
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHENIX phasing PHENIX refinement