9CDA | pdb_00009cda

Structure of type I-2 alpha-synuclein filament from multiple system atrophy


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d4.407
f_angle_d0.537
f_chiral_restr0.05
f_bond_d0.005
f_plane_restr0.002
Sample
Type I-2 alpha-synuclein filament from multiple system atrophy
Specimen Preparation
Sample Aggregation StateFILAMENT
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsWait time 30s, blot time 7.5s
3D Reconstruction
Reconstruction MethodHELICAL
Number of Particles12802
Reported Resolution (Å)3.3
Resolution MethodFSC 0.143 CUT-OFF
Other Details3D auto-refinement was performed using the type I-2 map from the first round of 3D classification low-pass filtered to 10 angstroms, allowing rise and ...3D auto-refinement was performed using the type I-2 map from the first 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 TypeHELICAL
Axial SymmetryC1
Axial Rise4.76
Angular Rotation-1.42
Map-Model Fitting and Refinement
Id1
Refinement Space
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)46
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)1800
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification105000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION4.0.1
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONCTFFIND4.1
MODEL FITTINGPHENIX
INITIAL EULER ASSIGNMENTRELION4.0.1
FINAL EULER ASSIGNMENTRELION4.0.1
CLASSIFICATIONRELION4.0.1
RECONSTRUCTIONRELION4.0.1
MODEL REFINEMENTPHENIX
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION257982Manual 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.