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Cryo-EM structure of ex vivo AA amyloid from renal tissue of a short hair cat deceased in a shelter
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.414 f_angle_d 0.816 f_chiral_restr 0.048 f_plane_restr 0.011 f_bond_d 0.002
Sample AA amyloid extracted from kidney of deceased cat
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 65000 Reported Resolution (Å) 3.3 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type HELICAL Axial Symmetry C2 Axial Rise 4.9043 Angular Rotation -1.29627
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol AB INITIO MODEL Refinement Target Overall B Value 76.7 Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON III (4k x 4k) Electron Dose (electrons/Å**2) 40
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TALOS ARCTICA Minimum Defocus (nm) 600 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 120000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION EPU 2.8 CTF CORRECTION CTFFIND 4 MODEL FITTING Coot 0.8.2 MODEL FITTING ISOLDE 1.1.0 MODEL FITTING UCSF ChimeraX 1.1.1 MODEL REFINEMENT PHENIX 1.19 INITIAL EULER ASSIGNMENT RELION 3.1 FINAL EULER ASSIGNMENT RELION 3.1 CLASSIFICATION RELION 3.1 RECONSTRUCTION RELION 3.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION