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Crystal structure of protein kinase CK2 catalytic subunit in complex with a Dibromo Dihydro Dibenzofuranone derivative
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 Initial drops were prepared by mixing two parts of a solution of 5 mg per mL CK2alpha1-335 including 1 mM 12c together with one part of the reservoir solution containing 30 % (weight per volume), PEG8000, 0.2 M (NH4)2SO4, and 0.1 M sodium cacodylate, pH 6.5. Crystallization was induced by microseeding.
Crystal Properties Matthews coefficient Solvent content 3.24 62.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.242 α = 90 b = 128.242 β = 90 c = 124.547 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 2023-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.8856 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.26 57.01 60.72 0.318 0.332 0.095 0.994 8.4 12 29856 41.27
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.26 2.341 4.32 3.726 3.889 1.106 0.647 1.9
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 2.26 57.01 1.34 29856 1454 60.37 0.2029 0.2011 0.2008 0.2389 0.2393 43.99
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 11.0737 f_angle_d 0.4397 f_chiral_restr 0.0418 f_plane_restr 0.0044 f_bond_d 0.0015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5576 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 102
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement