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Protein kinase CK2 bound to KDX1381
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Z83
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 33% polyethylene glycol methyl ether 5000, 0.2 M ammonium sulfate, 0.1 MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.9 57.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.385 α = 90 b = 125.385 β = 90 c = 126.399 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 2022-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9697 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 2.16 44.51 99.86 0.297 0.997 10.31 12.9 103197
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.16 2.237 0.22
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 2.16 44.51 1.88 103197 2105 99.72 0.2328 0.2319 0.2326 0.2754 0.2754
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 7.192 f_angle_d 0.979 f_chiral_restr 0.055 f_plane_restr 0.009 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5502 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 225
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing