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Cardiac amyloid fibrils extracted from a wild-type ATTR amyloidosis patient
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8E7D
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.971 f_angle_d 0.548 f_chiral_restr 0.05 f_plane_restr 0.007 f_bond_d 0.004
Sample cardiac amyloid fibril of wild-type transthyretin amyloidosis
Specimen Preparation Sample Aggregation State FILAMENT Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method HELICAL Number of Particles 50584 Reported Resolution (Å) 3.4 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type HELICAL Axial Symmetry C1 Axial Rise 4.898 Angular Rotation -1.245
Map-Model Fitting and Refinement Id 1 (8E7D) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Cross-correlation coefficient Overall B Value 71.63 Fitting Procedure Details Initial fitting was done using Coot with rigid body fit, then real space refinement for better fitting
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 40
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1700 Maximum Defocus (nm) 2300 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 EMAN2 2.31 CTF CORRECTION RELION 3.1 MODEL FITTING Coot 0.9.8.1 INITIAL EULER ASSIGNMENT RELION 3.1 FINAL EULER ASSIGNMENT RELION 3.1 CLASSIFICATION RELION 3.1 RECONSTRUCTION RELION 3.1 MODEL REFINEMENT PHENIX 20
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE