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PLK4 in complex with Compound 6 (3-hydroxy-N-(3-(pyridin-2-yl)-1H-pyrazol-4-yl)-8-azabicyclo[3.2.1]octane-8-carboxamide)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3COK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 8.5 293 0.1 M Tris pH 8.5,
16% ethanol , 5 mM DTT
Crystal Properties Matthews coefficient Solvent content 1.78 30.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.333 α = 90 b = 83.991 β = 90 c = 43.03 γ = 90
Symmetry Space Group P 21 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 EIGER X 16M 2022-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.9762 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.7 30 52.3 0.99 6.6 12.4 3441 68.35
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 2.7 3 0.7
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 2.7 29.22 1.34 3441 168 52.33 0.2451 0.2405 0.2559 0.3345 0.3467 76.64
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 15.6567 f_angle_d 0.4136 f_chiral_restr 0.0356 f_plane_restr 0.002 f_bond_d 0.0015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1876 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 28
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing