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Discovery of IRAK4 Inhibitors BAY1834845 and BAY1830839
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, HANGING DROP 293 0.1M sodium acetate buffer at pH 4.9, 1.5-1.7M ammonium citrate and 0.02M hexaaminecobalt(III)chloride
Crystal Properties Matthews coefficient Solvent content 2.7 54.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.258 α = 90 b = 117.97 β = 90 c = 139.861 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 2021-10-04 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 2.119 19.77 86.2 0.115 0.999 16.69 6.49 35635
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 2.12 2.25 0.701 1.66
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 THROUGHOUT in house model 2.119 19.768 35633 1782 86.176 0.241 0.2387 0.2497 0.2879 0.2951 60.235
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] -1.059 4.994 -3.935
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.303 r_dihedral_angle_4_deg 19.593 r_dihedral_angle_3_deg 14.972 r_lrange_other 14.255 r_lrange_it 14.24 r_scangle_it 11.666 r_scangle_other 11.639 r_mcangle_it 9.914 r_mcangle_other 9.913 r_scbond_it 8.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.303 r_dihedral_angle_4_deg 19.593 r_dihedral_angle_3_deg 14.972 r_lrange_other 14.255 r_lrange_it 14.24 r_scangle_it 11.666 r_scangle_other 11.639 r_mcangle_it 9.914 r_mcangle_other 9.913 r_scbond_it 8.016 r_scbond_other 7.999 r_mcbond_it 7.269 r_mcbond_other 7.267 r_dihedral_angle_1_deg 5.993 r_angle_refined_deg 1.239 r_angle_other_deg 1.11 r_symmetry_xyhbond_nbd_refined 0.26 r_symmetry_nbd_refined 0.239 r_nbd_other 0.221 r_nbd_refined 0.185 r_symmetry_nbd_other 0.177 r_nbtor_refined 0.156 r_xyhbond_nbd_refined 0.134 r_xyhbond_nbd_other 0.105 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.044 r_symmetry_xyhbond_nbd_other 0.025 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4344 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing