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Cryo-EM structure of hepatic amyloid fibril from a variant ATTRV122delta, single filament morphology
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8BDM
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.316 f_angle_d 0.579 f_chiral_restr 0.05 f_plane_restr 0.005 f_bond_d 0.003
Sample fibrils of ATTRV122delta
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 21384 Reported Resolution (Å) 2.9 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type HELICAL Axial Symmetry C1 Axial Rise 4.82 Angular Rotation -1.19
Map-Model Fitting and Refinement Id 1 (8BDM) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value 49.97 Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 2400 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 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 RELION 4.0 IMAGE ACQUISITION SerialEM 4.1.5 CTF CORRECTION CTFFIND 4.1 MODEL FITTING Coot 0.9.8.1 MODEL REFINEMENT PHENIX 1.20.1 INITIAL EULER ASSIGNMENT RELION 4.0 FINAL EULER ASSIGNMENT RELION 4.0 CLASSIFICATION RELION 4.0 RECONSTRUCTION RELION 4.0
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING ONLY 345559 Initial segment after extraction at box size of 300 pixel