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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
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.06 α = 90 b = 31.01 β = 107.696 c = 54.3 γ = 90
Symmetry Space Group C 1 2 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 ELECTRON CRYSTALLOGRAPHY MOLECULAR REPLACEMENT THROUGHOUT 4W8G 3 30.54 1.36 2436 129 73.84 0.2261 0.2229 0.241 0.28 0.3043 52.01
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 11.9175 f_angle_d 0.5243 f_chiral_restr 0.0425 f_plane_restr 0.0037 f_bond_d 0.003
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.refine refinement PHENIX refinement PHASER phasing
Sample Myeloid differentiation primary response protein MyD88
Specimen Preparation Sample Aggregation State 3D ARRAY Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method CRYSTALLOGRAPHY Number of Particles Reported Resolution (Å) Resolution Method DIFFRACTION PATTERN/LAYERLINES Other Details Refinement Type Symmetry Type 3D CRYSTAL Space Group Name Length a 99.06 Length b 31.01 Length c 31.01 Angle Alpha 90 Angle Beta 107.7 Angle Gamma 90
Map-Model Fitting and Refinement Id 1 Refinement Space Refinement Protocol OTHER Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type OTHER Electron Dose (electrons/Å**2) 0.08
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model JEOL 2100 Minimum Defocus (nm) Maximum Defocus (nm) Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode DIFFRACTION Specimen Holder Model Nominal Magnification Calibrated Magnification Source LAB6 Acceleration Voltage (kV) 200 Imaging Details
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE