8FF2

Amyloid-beta (1-40) fibrils derived from a CAA patient


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6SHS 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d10.634
f_angle_d0.41
f_chiral_restr0.044
f_bond_d0.005
f_plane_restr0.002
Sample
Fibrillar assembly of human Amyloid-beta 1-40 derived from vascular deposits in a cerebral amyloid angiopathy patient
Specimen Preparation
Sample Aggregation StateFILAMENT
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodHELICAL
Number of Particles59075
Reported Resolution (Å)2.87
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypeHELICAL
Axial SymmetryC1
Axial Rise2.44
Angular Rotation-178.83
Map-Model Fitting and Refinement
Id1 (6SHS)
Refinement SpaceREAL
Refinement ProtocolAB INITIO MODEL
Refinement Target
Overall B Value31.1
Fitting Procedure
Details
Data Acquisition
Detector TypeFEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)49.7
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TALOS ARCTICA
Minimum Defocus (nm)800
Maximum Defocus (nm)1400
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification92000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION3.1.1
IMAGE ACQUISITIONEPU
CTF CORRECTIONGctf1.06
CTF CORRECTIONRELION3.1.1
MODEL FITTINGCoot
MODEL REFINEMENTPHENIX1.19.1
MODEL REFINEMENTISOLDE1.4
INITIAL EULER ASSIGNMENTRELION3.1.1
FINAL EULER ASSIGNMENTRELION3.1.1
CLASSIFICATIONRELION3.1.1
RECONSTRUCTIONRELION3.1.1
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTIONPer-micrograph correction via Gctf. Aberration, magnification, and per-particle corrections via RELION.68357Manual helical picking and extraction