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Cryo-EM structure of amyloid fibril extracted from nerve of a variant ATTR V30M amyloidosis patient
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SDZ
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.507 f_angle_d 0.649 f_chiral_restr 0.052 f_bond_d 0.006 f_plane_restr 0.005
Specimen Preparation Sample Aggregation State FILAMENT Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details Blot-force 0, blotting time 3 sec
3D Reconstruction Reconstruction Method HELICAL Number of Particles 104108 Reported Resolution (Å) 3.36 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type HELICAL Axial Symmetry C1 Axial Rise 4.93 Angular Rotation -1.31
Map-Model Fitting and Refinement Id 1 (6SDZ) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 40
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 900 Maximum Defocus (nm) 2100 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Topaz IMAGE ACQUISITION EPU 3.5 CTF CORRECTION CTFFIND 4.1 MODEL FITTING Coot 0.9.8.1 INITIAL EULER ASSIGNMENT RELION 4.0 FINAL EULER ASSIGNMENT RELION 4.0 CLASSIFICATION RELION 4.0 RECONSTRUCTION RELION 4.0 MODEL REFINEMENT PHENIX 1.20.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE