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cryoEM structure of amyloid fibrils formed by human RIPK1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other
Sample hRIPK1 RHIM-mediated amyloid fibril
Specimen Preparation Sample Aggregation State HELICAL ARRAY Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details time 5.5s, blotting force 2
3D Reconstruction Reconstruction Method HELICAL Number of Particles 460173 Reported Resolution (Å) 2.57 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type HELICAL Axial Symmetry C1 Axial Rise 4.667 Angular Rotation -7.319
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value 66.05 Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOCONTINUUM (6k x 4k) Electron Dose (electrons/Å**2) 49.3
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 1600 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 165000 Calibrated Magnification Source LAB6 Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.6.0 IMAGE ACQUISITION EPU 3.8.0.7600 CTF CORRECTION cryoSPARC 4.6.0 INITIAL EULER ASSIGNMENT cryoSPARC 4.6.0 FINAL EULER ASSIGNMENT cryoSPARC 4.6.0 RECONSTRUCTION cryoSPARC 4.6.2 MODEL REFINEMENT Coot 0.9.2 MODEL REFINEMENT PHENIX 1.21
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 2814672