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Discovery of IRAK4 Inhibitor 40
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 pH 4.9, 2.13-2.145M sodium malonate
Crystal Properties Matthews coefficient Solvent content 2.72 54.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.725 α = 90 b = 118.573 β = 90 c = 138.709 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 PILATUS 6M 2013-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 2.167 46.303 99.7 0.138 0.998 10.85 5.01 38659
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 0.651 1.71
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 2.167 46.303 38633 1932 99.634 0.215 0.2133 0.2209 0.2513 0.2549 48.702
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] -0.289 2.981 -2.692
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.548 r_dihedral_angle_4_deg 22.357 r_dihedral_angle_3_deg 14.796 r_lrange_other 9.356 r_lrange_it 9.351 r_scangle_it 7.29 r_scangle_other 7.289 r_dihedral_angle_1_deg 6.009 r_mcangle_it 5.77 r_mcangle_other 5.769
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.548 r_dihedral_angle_4_deg 22.357 r_dihedral_angle_3_deg 14.796 r_lrange_other 9.356 r_lrange_it 9.351 r_scangle_it 7.29 r_scangle_other 7.289 r_dihedral_angle_1_deg 6.009 r_mcangle_it 5.77 r_mcangle_other 5.769 r_scbond_it 4.251 r_scbond_other 4.25 r_mcbond_it 3.577 r_mcbond_other 3.576 r_angle_refined_deg 1.22 r_angle_other_deg 1.107 r_nbd_other 0.172 r_nbd_refined 0.171 r_symmetry_nbd_other 0.167 r_symmetry_nbd_refined 0.167 r_symmetry_xyhbond_nbd_refined 0.163 r_nbtor_refined 0.151 r_xyhbond_nbd_refined 0.119 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.043 r_xyhbond_nbd_other 0.014 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4440 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing