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Crystal structure of IRAK4 kinase domain with compound 4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 291 0.2M Ammonium sulfate, 0.1M MES, pH6.9, 30% w/v PEG5000 MME
Crystal Properties Matthews coefficient Solvent content 2.47 50.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.85 α = 90 b = 140.49 β = 123.73 c = 87.94 γ = 90
Symmetry Space Group C 1 2 1
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 9M 2018-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97633 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.92 47.87 98.9 0.2 0.216 0.082 0.992 7.7 7 30999
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.92 3.08 99.9 0.868 0.935 0.346 0.852 7.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.92 47.87 29473 1524 98.83 0.21886 0.21643 0.2186 0.2655 0.2705 RANDOM 60.861
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] 3.29 2.04 -3.81 -1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.498 r_dihedral_angle_4_deg 22.938 r_dihedral_angle_3_deg 16.209 r_long_range_B_refined 10.985 r_long_range_B_other 10.985 r_scangle_other 7.93 r_mcangle_it 7.719 r_mcangle_other 7.718 r_dihedral_angle_1_deg 7.06 r_scbond_it 5.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.498 r_dihedral_angle_4_deg 22.938 r_dihedral_angle_3_deg 16.209 r_long_range_B_refined 10.985 r_long_range_B_other 10.985 r_scangle_other 7.93 r_mcangle_it 7.719 r_mcangle_other 7.718 r_dihedral_angle_1_deg 7.06 r_scbond_it 5.01 r_scbond_other 5.01 r_mcbond_it 5.006 r_mcbond_other 5.002 r_angle_refined_deg 1.511 r_angle_other_deg 1.188 r_chiral_restr 0.059 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9160 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms 146
Software Software Software Name Purpose REFMAC refinement Aimless data scaling REFMAC phasing XDS data reduction