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Structure of protein kinase CK2alpha mutant T127M 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 Reservoir: 200 mM Lithium sulphate, 100 mM Bis-tris, pH 6.5, 35 % PEG 3350
Protein concentrated to 5 mg per mL in 500 mM NaCl, 25 mM Tris-HCl, pH 8.5
Drop: 6 microliter protein, 2 microliter reservoir solution
Crystal Properties Matthews coefficient Solvent content 2.69 54.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.099 α = 90 b = 128.099 β = 90 c = 124.285 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 EIGER2 X 9M 2025-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.87313 ESRF ID30B
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 2.25 73.202 69 0.317 0.997 9.4 25.6 34073 28.82
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 2.253 2.481 2.227 0.698 1.5
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 2.25 73.2 1.34 34020 2005 68.91 0.2069 0.2046 0.2043 0.2449 0.2438 36.67
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 12.4104 f_angle_d 0.4841 f_chiral_restr 0.0434 f_plane_restr 0.0051 f_bond_d 0.0022
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5569 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms 50
Software Software Software Name Purpose PHASER phasing PHENIX refinement XDS data reduction Aimless data scaling STARANISO data scaling autoPROC data processing