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Structure of protein kinase CK2alpha mutant K198R associated with the Okur-Chung Neurodevelopmental Syndrome
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 The crystallization drops were composed of a 1:1 mix of the protein solution (5 mg/mL in 500 mM NaCl, 25 mM TRIS/HCl buffer, pH 8,5) and the reservoir solution containing [0.2 M lithium sulfate, 25 % (w/v) PEG 3350 and 0.1 M Bis/TRIS/HCl, pH 6.5]. The crystals were optimized by macroseeding and transferred into a cryo-protectant solution composed of 70 microliter of the reservoir solution and 30 microliter ethylene glycol.
Crystal Properties Matthews coefficient Solvent content 3.16 61.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.824 α = 90 b = 127.824 β = 90 c = 123.18 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 PILATUS3 X 2M 2021-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87313 ESRF ID23-2
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 1.774 88.698 66.5 0.587 0.587 0.594 0.087 0.99 18.1 44.4 65649 3.97
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 1.774 1.98 12 2.814 2.814 2.85 0.448 0.709 1.8
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 2PVR 1.77 50.9 1.35 65627 1332 66.51 0.1809 0.1802 0.1803 0.2183 0.2177 20.22
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 11.5978 f_angle_d 0.6474 f_chiral_restr 0.0465 f_plane_restr 0.0067 f_bond_d 0.0038
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5612 Nucleic Acid Atoms Solvent Atoms 666 Heterogen Atoms 83
Software Software Software Name Purpose PHENIX refinement autoPROC data processing autoPROC data reduction STARANISO data scaling PHASER phasing