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Cryo-EM structure of ex vivo Sup35 prion fibrils from yeast carrying "strong" [PSI+] variant
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s)
Type
Source
Accession Code
Details
other
Other
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
14.911
f_angle_d
0.453
f_chiral_restr
0.035
f_bond_d
0.005
f_plane_restr
0.002
Sample
Ex vivo Sup35 prion fibrils from yeast carrying strong [PSI+] variant
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
50658
Reported Resolution (Å)
2.7
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
HELICAL
Axial Symmetry
C1
Axial Rise
4.782
Angular Rotation
-1.388
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-l ...
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/Å**2)
52
Imaging Experiment
1
Date of Experiment
Temperature (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
EM Software
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
1259000
Filaments were automatically picked with crYOLO using an inter-box step of 24 angstrom (five helical units per step).