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Cryo-EM structure of amyloid fibril extracted from thyroid of a variant ATTR T60A amyloidosis patient 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9D23
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.674 f_angle_d 0.567 f_chiral_restr 0.05 f_plane_restr 0.008 f_bond_d 0.002
Sample Amyloid fibril from thyroid of a variant ATTR T60A amyloidosis patient
Specimen Preparation Sample Aggregation State HELICAL ARRAY Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method HELICAL Number of Particles 133439 Reported Resolution (Å) 2.98 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type HELICAL Axial Symmetry C1 Axial Rise 4.79 Angular Rotation -1.23
Map-Model Fitting and Refinement Id 1 (9d23) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 900 Maximum Defocus (nm) 2200 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 SerialEM 3.8 CTF CORRECTION RELION 4.0 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
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE 675457 particle boxsize of 256 px