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SFX structure of the MyD88 TIR domain higher-order assembly (solved, rebuilt and refined using an identical protocol to the MicroED structure of the MyD88 TIR domain higher-order assembly)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4W8G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 310 MAL TIR (0.5-3 mM) incubated with MyD88 TIR (60-100 mM) in 10 mM HEPES pH 7.5-8, 150 mM NaCl at 310K
Crystal Properties Matthews coefficient Solvent content 2.31 46.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.4 α = 90 b = 31.5 β = 107.4 c = 54.5 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 300 PIXEL CS-PAD CXI-1 2015-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE CXI 1.3 SLAC LCLS CXI
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.3 30.94 95.8 0.9 2.6 1 7118 32.47
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 78.1 0.36 1.1 1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4W8G 2.3 30.93 1.91 7040 353 94.42 0.2414 0.2392 0.2384 0.2806 0.2801 45.6
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 9.8881 f_angle_d 0.3696 f_chiral_restr 0.0389 f_plane_restr 0.0026 f_bond_d 0.0013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1133 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PHASER phasing CrystFEL data scaling Aimless data reduction