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Structure of protein kinase CK2alpha mutant H160R 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 293 200 mM Li2SO4, 100 mM Bis-tris/HCl, pH 6.5, 25 % PEG 3350
Protein 5 mg per mL in 500 mM NaCl, 25 mM TRIS/HCl, pH 8.5
2 parts protein mixed with one part Reservoir
Soaking with AMPPNP/MgCl2
Crystal Properties Matthews coefficient Solvent content 2.73 54.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.712 α = 90 b = 128.712 β = 90 c = 124.79 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 2023-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.91840 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 2.088 91.013 65.2 0.388 0.996 9.1 11.2 40809 32.62
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 2.088 2.39 4.137 0.386 1.6
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 2.09 91.01 1.34 40781 2037 65.11 0.1896 0.187 0.1877 0.2374 0.2378 42.41
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 13.9741 f_angle_d 0.7096 f_chiral_restr 0.0477 f_plane_restr 0.0061 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5583 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 126
Software Software Software Name Purpose autoPROC data processing PHENIX refinement XDS data reduction Aimless data scaling STARANISO data scaling