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Structure of in-vivo formed alpha-synuclein fibrils purified from a M83+/- mouse brain injected with recombinant 1B fibrils
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9EUU
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.866 f_angle_d 0.766 f_chiral_restr 0.054 f_bond_d 0.004 f_plane_restr 0.004
Sample Alpha-synuclein fibril purified from the brain of a 1B-injected M83+/- mouse
Specimen Preparation Sample Aggregation State FILAMENT Vitrification Instrument LEICA EM GP Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method HELICAL Number of Particles 1913 Reported Resolution (Å) 3.8 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type HELICAL Axial Symmetry C1 Axial Rise 2.4 Angular Rotation 179.55
Map-Model Fitting and Refinement Id 1 (9EUU, 9EUU) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details A rigid-body fit was done using ChimeraX and a subsequent jiggle fit and all-atom refinement was done in Coot.
Data Acquisition Detector Type FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2200 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 165000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION RELION 4.0.0 PARTICLE SELECTION cryoSPARC 4.7.0 IMAGE ACQUISITION EPU CTF CORRECTION CTFFIND 4.1 MODEL FITTING Coot 0.9.8.96 MODEL FITTING UCSF ChimeraX 1.6 RECONSTRUCTION RELION 4.0.0 MODEL REFINEMENT PHENIX 1.21.2
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 3556 Particles selected by manual picking of fibril start and end points