ELECTRON MICROSCOPY

Sample

Ex vivo Sup35 prion fibrils from yeast carrying strong [PSI+] variant

Specimen Preperation
Sample Aggregation State FILAMENT
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details ?
3D Reconstruction
Reconstruction Method HELICAL
Number of Particles 50658
Reported Resolution (Å) 2.70
Resolution Method FSC 0.143 CUT-OFF
Other Details ?
Refinement Type
Symmetry Type HELICAL
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol FLEXIBLE FIT
Refinement Target Maximum likelihood with map correlation
Overall B Value 59.7
Fitting Procedure ?
Details A single protomer was built de novo into the sharpened map in Coot, with unambiguous sequence assignment. The built protomer was stacked into a five-layer segment by rigid-body placement in UCSF Chimera, and the resulting model was refined in PHENIX real-space refine with NCS constraints between the five chains and individual ADPs.
Data Acquisition
Detector Type GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å2) 52
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model TFS KRIOS
Minimum Defocus (nm) 700
Maximum Defocus (nm) 2000
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS 0.01
Imaging Mode BRIGHT FIELD
Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification 81000
Calibrated Magnification 57937
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details Cs corrected, 3x3 holes (2 exposures per hole) image-shift data acquisition strategy
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION crYOLO 1.9
IMAGE ACQUISITION SerialEM 4.055
CTF CORRECTION CTFFIND 4.1
MODEL FITTING PHENIX 1.21.2_5419
INITIAL EULER ASSIGNMENT cryoSPARC 4.6
FINAL EULER ASSIGNMENT cryoSPARC 4.6
CLASSIFICATION cryoSPARC 4.6
RECONSTRUCTION cryoSPARC 4.6
MODEL REFINEMENT PHENIX 1.21.2_5419
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?
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