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Discovery of IRAK4 Inhibitor 38
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Other in house model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.9 293 0.1M sodium acetate buffer pH 4.9, 1.5-1.7M ammonium citrate, 0.02M hexaaminecobalt(III)chloride
Crystal Properties Matthews coefficient Solvent content 2.78 55.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.194 α = 90 b = 118.899 β = 90 c = 140.475 γ = 90
Symmetry Space Group I 2 2 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 2021-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9763 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.17 49.88 99.9 0.119 0.999 13.77 13.75 39306
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 2.17 2.3 0.767
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE in house model 2.171 49.875 39289 1965 99.898 0.242 0.2384 0.244 0.3059 0.3059 77.038
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] -8.899 8.235 0.664
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.338 r_dihedral_angle_4_deg 25.87 r_dihedral_angle_3_deg 23.671 r_lrange_it 12.842 r_lrange_other 12.839 r_scangle_it 10.794 r_scangle_other 10.792 r_scbond_it 7.431 r_scbond_other 7.429 r_mcangle_it 7.333
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.338 r_dihedral_angle_4_deg 25.87 r_dihedral_angle_3_deg 23.671 r_lrange_it 12.842 r_lrange_other 12.839 r_scangle_it 10.794 r_scangle_other 10.792 r_scbond_it 7.431 r_scbond_other 7.429 r_mcangle_it 7.333 r_mcangle_other 7.333 r_dihedral_angle_1_deg 6.611 r_mcbond_it 5.12 r_mcbond_other 5.116 r_angle_refined_deg 1.767 r_angle_other_deg 1.356 r_symmetry_nbd_refined 0.632 r_nbd_other 0.255 r_nbd_refined 0.228 r_symmetry_nbd_other 0.221 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.157 r_symmetry_nbtor_other 0.088 r_symmetry_xyhbond_nbd_refined 0.083 r_chiral_restr 0.073 r_symmetry_xyhbond_nbd_other 0.031 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.005 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4451 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing