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Crystal Structure of IRAK4 kinase in complex with the inhibitor CA-4948
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OIB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 298 0.1 M sodium acetate pH 5.4, 2.3 M sodium malonate
Crystal Properties Matthews coefficient Solvent content 2.54 51.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.759 α = 90 b = 138.589 β = 124.5 c = 87.359 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 CCD OXFORD ONYX CCD 2019-12-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 1 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.44 30 98.9 0.133 0.8 6.2 2.8 51404
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.44 2.57 0.7 0.8 2.8
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 (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 2OIB 2.44 30 48865 2535 98.8 0.1983 0.1955 0.2035 0.2533 0.2526 RANDOM 64.799
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] 1.45 1.59 -3.9 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.957 r_dihedral_angle_4_deg 19.649 r_dihedral_angle_3_deg 15.987 r_dihedral_angle_1_deg 5.71 r_angle_refined_deg 1.522 r_angle_other_deg 1.03 r_chiral_restr 0.092 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.957 r_dihedral_angle_4_deg 19.649 r_dihedral_angle_3_deg 15.987 r_dihedral_angle_1_deg 5.71 r_angle_refined_deg 1.522 r_angle_other_deg 1.03 r_chiral_restr 0.092 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8976 Nucleic Acid Atoms Solvent Atoms 402 Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling MOLREP phasing