6IC3
AL amyloid fibril from a lambda 1 light chain
ELECTRON MICROSCOPY
Sample |
---|
Amyloid fibril of an antibody lambda 1 light chain |
Specimen Preparation | |
---|---|
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 |
Axial Symmetry | C1 |
Axial Rise | 4.81 |
Angular Rotation | 0.58 |
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 durin ... |
Data Acquisition | |||||||||
---|---|---|---|---|---|---|---|---|---|
Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 32 |
Imaging Experiment | 1 |
---|---|
Date of Experiment | |
Temperature (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 |
EM Software | ||
---|---|---|
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 | 119395 | manual selection. Sigma contrast 3, lowpass filter 20 A |