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CryoEM structure of AL55 amyloid fibrils extracted from the kidney of an AL amyloidosis patient.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HUD
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.165 f_angle_d 0.932 f_chiral_restr 0.059 f_plane_restr 0.005 f_bond_d 0.002
Sample Renal AL55 amyloid fibrils
Specimen Preparation Sample Aggregation State FILAMENT Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method HELICAL Number of Particles 49091 Reported Resolution (Å) 4 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type HELICAL Axial Symmetry C1 Axial Rise 4.9 Angular Rotation -1.63 Axial Symmetry C1 Axial Rise 4.9 Angular Rotation -1.63
Map-Model Fitting and Refinement Id 1 (6HUD) Refinement Space REAL Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON III (4k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TALOS ARCTICA Minimum Defocus (nm) 800 Maximum Defocus (nm) 2500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION RELION 3.1 CTF CORRECTION CTFFIND 4.1 MODEL FITTING UCSF ChimeraX CLASSIFICATION RELION 3.1 RECONSTRUCTION RELION 3.1 MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 98829