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Crystal structure of IRAK4 kinase domain with compound 9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other internal structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 1.8M ammonium citrate,
1.75mM compound (1.8% DMSO)
Crystal Properties Matthews coefficient Solvent content 2.49 50.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.87 α = 90 b = 140.68 β = 124 c = 89.02 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 PILATUS 6M 2021-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97915 SSRF BL18U1
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 2.09 49.14 99.86 0.1389 0.1507 0.0578 0.997 13.07 6.8 85963 35.99
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 2.09 2.165 99.95 1.17 1.265 0.477 0.668 2.35 7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.09 49.14 81617 4334 99.9 0.17014 0.16814 0.20754 0.2076 RANDOM 43.936
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] 0.94 0.83 -3.12 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.431 r_dihedral_angle_4_deg 23.428 r_dihedral_angle_3_deg 16.026 r_long_range_B_other 10.819 r_long_range_B_refined 10.808 r_scangle_other 8.267 r_dihedral_angle_1_deg 6.304 r_mcangle_it 6.117 r_mcangle_other 6.116 r_scbond_it 5.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.431 r_dihedral_angle_4_deg 23.428 r_dihedral_angle_3_deg 16.026 r_long_range_B_other 10.819 r_long_range_B_refined 10.808 r_scangle_other 8.267 r_dihedral_angle_1_deg 6.304 r_mcangle_it 6.117 r_mcangle_other 6.116 r_scbond_it 5.43 r_scbond_other 5.43 r_mcbond_it 4.146 r_mcbond_other 4.146 r_angle_refined_deg 1.589 r_angle_other_deg 1.34 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 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 9397 Nucleic Acid Atoms Solvent Atoms 619 Heterogen Atoms 175
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing