ELECTRON MICROSCOPY

Sample

Amyloid fibril of an antibody lambda 1 light chain

Specimen Preperation
Sample Aggregation State FILAMENT
Vitrification Instrument GATAN CRYOPLUNGE 3
Cryogen Name ETHANE
Sample Vitrification Details blotted from the backside for 4 s before plunging
3D Reconstruction
Reconstruction Method HELICAL
Number of Particles 32677
Reported Resolution (Å) 3.3
Resolution Method FSC 0.143 CUT-OFF
Other Details ?
Refinement Type
Symmetry Type HELICAL
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol OTHER
Refinement Target REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Overall B Value 111.4
Fitting Procedure ?
Details Refinement strategy included global minimization and local grid search and ADP were refined. Secondary structure restraints and NCS were applied during refinement.
Data Acquisition
Detector Type GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å2) 32
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TITAN KRIOS
Minimum Defocus (nm) ?
Maximum Defocus (nm) ?
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 ?
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
IMAGE ACQUISITION SerialEM ?
CTF CORRECTION Gctf 1.06
MODEL FITTING Warp 8.0
MODEL FITTING Coot 0.8.9
INITIAL EULER ASSIGNMENT RELION 2.1.0
CLASSIFICATION RELION 2.1.0
RECONSTRUCTION RELION 2.1.0
MODEL REFINEMENT PHENIX 1.14.3260
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION CTF was estimated from the non-dose-weighted micrographs