ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 6E26 | |
| Sample |
|---|
| Helical assembly of the CARD9 CARD. |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | FILAMENT |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Sample was incubated on the grid for 1 minute, subsequently washed/blotted 6 times in buffer, followed by addition of 3.5 ul buffer, which was blotted ... |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | HELICAL |
| Number of Particles | 31908 |
| Reported Resolution (Å) | 4 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | A 5.0 A high-resolution limit was used for particle alignment in frealign. |
| Refinement Type | |
| Symmetry Type | HELICAL |
| Axial Symmetry | C1 |
| Axial Rise | 5.11 |
| Angular Rotation | -101.6 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (6E26) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | "Fit in map" in UCSF Chimera was used to fit the previously determined, lowest energy NMR solution structure (PDB ID 6E26) into the sharpened density ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 50.9 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 1250 |
| Maximum Defocus (nm) | 2500 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.7 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | 130000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | EMAN2 | |
| PARTICLE SELECTION | RELION | 2.1 |
| IMAGE ACQUISITION | SerialEM | |
| CTF CORRECTION | CTFFIND | |
| MODEL FITTING | UCSF Chimera | |
| MODEL REFINEMENT | PHENIX | |
| MODEL REFINEMENT | Coot | |
| INITIAL EULER ASSIGNMENT | RELION | 2.1 |
| INITIAL EULER ASSIGNMENT | FREALIGN | |
| FINAL EULER ASSIGNMENT | FREALIGN | 9.11 |
| CLASSIFICATION | FREALIGN | 9.11 |
| RECONSTRUCTION | FREALIGN | 9.11 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 141592 | Filaments were manually selected using e2helixboxer.py. Segments were extracted from filaments using RELION, using a 30 A shift between particles. | ||
