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The Crystal Structure of IRAK4 from Biortus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EGF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M Ammonium sulfate,0.1M BisTris,5.5,25% w/vPEG 3350
Crystal Properties Matthews coefficient Solvent content 2.2 44.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.449 α = 90 b = 93.061 β = 99.146 c = 60.925 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 2021-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 46.53 99.7 0.147 6.8 4.1 19106
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 0.515
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2 46.53 19102 973 99.635 0.183 0.18 0.1912 0.2363 0.2481 31.171
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] -1.004 -1.101 2.932 -1.497
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.825 r_dihedral_angle_4_deg 22.93 r_lrange_other 14.517 r_lrange_it 14.483 r_scangle_it 13.021 r_scangle_other 13.011 r_dihedral_angle_3_deg 11.573 r_scbond_it 10.545 r_scbond_other 10.528 r_mcangle_it 8.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.825 r_dihedral_angle_4_deg 22.93 r_lrange_other 14.517 r_lrange_it 14.483 r_scangle_it 13.021 r_scangle_other 13.011 r_dihedral_angle_3_deg 11.573 r_scbond_it 10.545 r_scbond_other 10.528 r_mcangle_it 8.42 r_mcangle_other 8.418 r_mcbond_it 7.358 r_mcbond_other 7.357 r_dihedral_angle_1_deg 5.415 r_angle_refined_deg 1.151 r_angle_other_deg 1.075 r_nbd_refined 0.154 r_symmetry_nbd_other 0.153 r_nbtor_refined 0.144 r_nbd_other 0.113 r_symmetry_nbd_refined 0.11 r_xyhbond_nbd_refined 0.099 r_symmetry_xyhbond_nbd_refined 0.086 r_symmetry_nbtor_other 0.071 r_chiral_restr 0.038 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2290 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing