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Structure of type II-2 alpha-synuclein filament from multiple system atrophy
ELECTRON MICROSCOPY
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
4.715
f_angle_d
0.474
f_chiral_restr
0.051
f_bond_d
0.006
f_plane_restr
0.002
Sample
Type II-2 alpha-synuclein filament from multiple system atrophy
Specimen Preparation
Sample Aggregation State
FILAMENT
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
Wait time 30s, blot time 7.5s
3D Reconstruction
Reconstruction Method
HELICAL
Number of Particles
31115
Reported Resolution (Å)
3.2
Resolution Method
FSC 0.143 CUT-OFF
Other Details
3D auto-refinement was performed using the best type II-2 map from the final round of 3D classification low-pass filtered to 10 angstroms, allowing ri ...
3D auto-refinement was performed using the best type II-2 map from the final round of 3D classification low-pass filtered to 10 angstroms, allowing rise and twist parameters to vary. The refined map was subject to standard post-processing in RELION.
Refinement Type
Symmetry Type
HELICAL
Axial Symmetry
C1
Axial Rise
4.76
Angular Rotation
-1.35
Map-Model Fitting and Refinement
Id
1
Refinement Space
Refinement Protocol
FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector Type
GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)
46
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
TFS KRIOS
Minimum Defocus (nm)
800
Maximum Defocus (nm)
1800
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
2.7
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
105000
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
EM Software
Task
Software Package
Version
PARTICLE SELECTION
RELION
4.0.1
IMAGE ACQUISITION
SerialEM
CTF CORRECTION
CTFFIND
4.1
MODEL FITTING
PHENIX
MODEL REFINEMENT
PHENIX
INITIAL EULER ASSIGNMENT
RELION
4.0.1
FINAL EULER ASSIGNMENT
RELION
4.0.1
CLASSIFICATION
RELION
4.0.1
RECONSTRUCTION
RELION
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
257982
Manual picking followed by particle extraction (box size 900px binned to 300px) resulted in 257982 segments, which were subject to reference-free 2D classification to give 255032 remaining segments. These were re-extracted (box size 288px) without binning.