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Discovery of IRAK4 Inhibitor 23
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 4.9 293 0.1M sodium acetate buffer pH 4.9, 2.13-2.145M sodium malonate
Crystal Properties Matthews coefficient Solvent content 2.82 56.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.864 α = 90 b = 118.789 β = 90 c = 138.136 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 2013-11-13 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 2.46 46.354 99.8 0.074 0.999 17.3 5.5 146185
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.46 2.6 100 0.491 0.926
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 2.464 46.354 26316 1316 99.392 0.201 0.1988 0.2057 0.2429 0.2423 56.279
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] -0.337 3.653 -3.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.827 r_dihedral_angle_4_deg 26.04 r_dihedral_angle_3_deg 17.607 r_lrange_other 11.908 r_lrange_it 11.906 r_scangle_other 9.523 r_scangle_it 9.522 r_mcangle_it 8.075 r_mcangle_other 8.074 r_scbond_other 6.124
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.827 r_dihedral_angle_4_deg 26.04 r_dihedral_angle_3_deg 17.607 r_lrange_other 11.908 r_lrange_it 11.906 r_scangle_other 9.523 r_scangle_it 9.522 r_mcangle_it 8.075 r_mcangle_other 8.074 r_scbond_other 6.124 r_scbond_it 6.123 r_dihedral_angle_1_deg 5.699 r_mcbond_it 5.291 r_mcbond_other 5.289 r_angle_refined_deg 1.274 r_angle_other_deg 1.091 r_symmetry_xyhbond_nbd_refined 0.22 r_nbd_refined 0.168 r_symmetry_nbd_other 0.168 r_nbd_other 0.162 r_nbtor_refined 0.15 r_symmetry_nbd_refined 0.112 r_xyhbond_nbd_refined 0.107 r_xyhbond_nbd_other 0.103 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.041 r_bond_refined_d 0.003 r_gen_planes_refined 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 4354 Nucleic Acid Atoms Solvent Atoms 70 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing