ELECTRON MICROSCOPY

Sample

amyloid-beta(1-40) fibrils derived from human AD brain

Specimen Preperation
Sample Aggregation State FILAMENT
Vitrification Instrument LEICA PLUNGER
Cryogen Name ETHANE
Sample Vitrification Details The grids were preblotted for 10 seconds and blotted for 6 seconds before plunging.
3D Reconstruction
Reconstruction Method HELICAL
Number of Particles 14775
Reported Resolution (Å) 2.77
Resolution Method FSC 0.143 CUT-OFF
Other Details A modified version of RELION 3.0-beta was used for the reconstruction. The modified version allowed local averaging of the rotation angle. Final reconstruction used 2-fold screw symmetry.
Refinement Type
Symmetry Type HELICAL
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol AB INITIO MODEL
Refinement Target ?
Overall B Value ?
Fitting Procedure ?
Details Xplor-NIH was used to combine EM density with phi/psi restraints from NMR chemical shifts (from Talos-N Version 4.21 Rev 2016.343.11.31).
Data Acquisition
Detector Type GATAN K2 QUANTUM (4k x 4k)
Electron Dose (electrons/Å2) 73.5
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model TFS KRIOS
Minimum Defocus (nm) -500
Maximum Defocus (nm) -3000
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 130000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details Preliminary grid screening was done manually in FEI T12.
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION RELION 3.0
IMAGE ACQUISITION SerialEM v3.7
CTF CORRECTION Gctf ?
MODEL FITTING Coot 0.8.9
MODEL REFINEMENT X-PLOR 2.53
INITIAL EULER ASSIGNMENT RELION 3.0
INITIAL EULER ASSIGNMENT MATLAB ?
CLASSIFICATION RELION custom
RECONSTRUCTION RELION custom
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION The correction was done in Gctf and is corrected for amplitude. Per -particle CTF refinement was done prior to final reconstruction.

SOLID-STATE NMR

NMR Experiment
Experiment Type Sample Contents Ionic Strength Solvent pH Pressure Temprature (K)
1 3D NCACX 100 uM U-15N,13C amyloid-beta(1-40), phosphate buffer 10 phosphate buffer 7.4 1 297
2 3D NCOCX 100 uM U-15N,13C amyloid-beta(1-40), phosphate buffer 10 phosphate buffer 7.4 1 297
3 3D CANCX 100 uM U-15N,13C amyloid-beta(1-40), phosphate buffer 10 phosphate buffer 7.4 1 297
4 3D CONCX 100 uM U-15N,13C amyloid-beta(1-40), phosphate buffer 10 phosphate buffer 7.4 1 297
5 2D 13C-13C 100 uM U-15N,13C amyloid-beta(1-40), phosphate buffer 10 phosphate buffer 7.4 1 297
NMR Spectrometer Information
Spectrometer Manufacturer Model Field Strength
1 Varian InfinityPlus 600
NMR Refinement
Method Details Software
simulated annealing phi/psi from TalosN & EM density used as restraints 3
NMR Ensemble Information
Conformer Selection Criteria structures with the least restraint violations
Conformers Calculated Total Number 60
Conformers Submitted Total Number 10
Representative Model 1 (lowest energy)
Computation: NMR Software
# Classification Version Software Name Author
1 processing ? NMRPipe Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
2 chemical shift assignment ? Sparky Goddard
3 refinement 2.53 X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore