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 | |
