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Crystal structure of IRAK4 with compound 1, an analog of KT-474 TBM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NRU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 298 50mM HEPES, pH 7.5, 100mM NaCl, 5mM DTT
Crystal Properties Matthews coefficient Solvent content 2.73 55.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.603 α = 90 b = 121.7 β = 90 c = 140.424 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS 6M 2018-06-04 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97930 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 2.05 41.32 100 0.069 0.043 0.017 0.998 28.8 6.5 94061
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 2.05 2.12 100 0.878 0.957 0.379 0.782 2.1 6.3
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 2.05 41.28 89234 4827 99.48 0.16008 0.1576 0.1661 0.2063 0.2004 RANDOM 45.771
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] -19.56 47.72 -28.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.043 r_dihedral_angle_4_deg 26.525 r_dihedral_angle_3_deg 15.561 r_dihedral_angle_1_deg 6.062 r_long_range_B_refined 5.752 r_long_range_B_other 5.752 r_scangle_other 5.321 r_mcangle_it 4.556 r_mcangle_other 4.556 r_scbond_it 4.216
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.043 r_dihedral_angle_4_deg 26.525 r_dihedral_angle_3_deg 15.561 r_dihedral_angle_1_deg 6.062 r_long_range_B_refined 5.752 r_long_range_B_other 5.752 r_scangle_other 5.321 r_mcangle_it 4.556 r_mcangle_other 4.556 r_scbond_it 4.216 r_scbond_other 4.216 r_mcbond_it 3.621 r_mcbond_other 3.617 r_rigid_bond_restr 1.269 r_angle_refined_deg 1.257 r_angle_other_deg 1.196 r_chiral_restr 0.052 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9312 Nucleic Acid Atoms Solvent Atoms 481 Heterogen Atoms 172
Software Software Software Name Purpose REFMAC refinement SCALA data scaling HKL-3000 data reduction PHASER phasing PDB_EXTRACT data extraction