6W0O

Amyloid-beta(1-40) fibril derived from Alzheimer's disease cortical tissue


ELECTRON MICROSCOPY - SOLID-STATE NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
13D NCACX100 uM U-15N,13C amyloid-beta(1-40)phosphate buffer10 mM7.41 atm297Varian InfinityPlus 600
23D NCOCX100 uM U-15N,13C amyloid-beta(1-40)phosphate buffer10 mM7.41 atm297Varian InfinityPlus 600
33D CANCX100 uM U-15N,13C amyloid-beta(1-40)phosphate buffer10 mM7.41 atm297Varian InfinityPlus 600
43D CONCX100 uM U-15N,13C amyloid-beta(1-40)phosphate buffer10 mM7.41 atm297Varian InfinityPlus 600
52D 13C-13C100 uM U-15N,13C amyloid-beta(1-40)phosphate buffer10 mM7.41 atm297Varian InfinityPlus 600
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1VarianInfinityPlus600
NMR Refinement
MethodDetailsSoftware
simulated annealingphi/psi from TalosN & EM density used as restraintsX-PLOR NIH
NMR Ensemble Information
Conformer Selection Criteriastructures with the least restraint violations
Conformers Calculated Total Number60
Conformers Submitted Total Number10
Representative Model1 (lowest energy)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1processingNMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
2chemical shift assignmentSparkyGoddard
3refinementX-PLOR NIH2.53Schwieters, Kuszewski, Tjandra and Clore
Sample
amyloid-beta(1-40) fibrils derived from human AD brain
Specimen Preparation
Sample Aggregation StateFILAMENT
Vitrification InstrumentLEICA PLUNGER
Cryogen NameETHANE
Sample Vitrification DetailsThe grids were preblotted for 10 seconds and blotted for 6 seconds before plunging.
3D Reconstruction
Reconstruction MethodHELICAL
Number of Particles14775
Reported Resolution (Å)2.77
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsA 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 TypeHELICAL
Axial SymmetryC1
Axial Rise2.45
Angular Rotation179.66
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolAB INITIO MODEL
Refinement Target
Overall B Value
Fitting Procedure
DetailsXplor-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 TypeGATAN K2 QUANTUM (4k x 4k)
Electron Dose (electrons/Å**2)73.5
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)-500
Maximum Defocus (nm)-3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification130000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging DetailsPreliminary grid screening was done manually in FEI T12.
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION3.0
IMAGE ACQUISITIONSerialEMv3.7
CTF CORRECTIONGctf
MODEL FITTINGCoot0.8.9
MODEL REFINEMENTX-PLOR2.53
INITIAL EULER ASSIGNMENTRELION3.0
INITIAL EULER ASSIGNMENTMATLAB
CLASSIFICATIONRELIONcustom
RECONSTRUCTIONRELIONcustom
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTIONThe correction was done in Gctf and is corrected for amplitude. Per -particle CTF refinement was done prior to final reconstruction.19790The particles were picked using Relion manual pick, with a 20A low pass filter and particle diameter of 30A.