Amyloid-beta(1-40) fibril derived from Alzheimer's disease cortical tissue
ELECTRON MICROSCOPY - SOLID-STATE NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
3D NCACX
100 uM U-15N,13C amyloid-beta(1-40)
phosphate buffer
10 mM
7.4
1 atm
297
Varian InfinityPlus 600
2
3D NCOCX
100 uM U-15N,13C amyloid-beta(1-40)
phosphate buffer
10 mM
7.4
1 atm
297
Varian InfinityPlus 600
3
3D CANCX
100 uM U-15N,13C amyloid-beta(1-40)
phosphate buffer
10 mM
7.4
1 atm
297
Varian InfinityPlus 600
4
3D CONCX
100 uM U-15N,13C amyloid-beta(1-40)
phosphate buffer
10 mM
7.4
1 atm
297
Varian InfinityPlus 600
5
2D 13C-13C
100 uM U-15N,13C amyloid-beta(1-40)
phosphate buffer
10 mM
7.4
1 atm
297
Varian InfinityPlus 600
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
X-PLOR NIH
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
X-PLOR NIH
2.53
Schwieters, Kuszewski, Tjandra and Clore
Sample
amyloid-beta(1-40) fibrils derived from human AD brain
Specimen Preparation
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 rec ...
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
Axial Symmetry
C1
Axial Rise
2.45
Angular Rotation
179.66
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/Å**2)
73.5
Imaging Experiment
1
Date of Experiment
Temperature (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.
EM Software
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.
19790
The particles were picked using Relion manual pick, with a 20A low pass filter and particle diameter of 30A.