ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 7ZL4 | |
| Sample |
|---|
| Csu pilus rod type 2 stack |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | 2D ARRAY |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 687088 |
| Reported Resolution (Å) | 4.7 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Local Refinement allowed generating a single map without individual particles flipping and settling into pseudosymmetric orientations. |
| Refinement Type | |
| Symmetry Type | POINT |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (7ZL4) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | |||||
| Overall B Value | 330.69 | ||||
| Fitting Procedure | |||||
| Details | UCSF Chimera was used to first fit the subunits into the single native pilus rod map (PDB Accession ID: 9I37) and average their relative angles, and i ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 59.848 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 400 |
| Maximum Defocus (nm) | 1600 |
| 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 | 105000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | v4.5.3 |
| IMAGE ACQUISITION | EPU | v3.60 |
| CTF CORRECTION | cryoSPARC | v4.5.3 |
| MODEL FITTING | UCSF Chimera | 1.15 |
| MODEL FITTING | Coot | 0.8.9.2 EL |
| MODEL REFINEMENT | PHENIX | 1.20.1_4487: |
| INITIAL EULER ASSIGNMENT | cryoSPARC | v4.5.3 |
| FINAL EULER ASSIGNMENT | cryoSPARC | v4.5.3 |
| CLASSIFICATION | cryoSPARC | v4.5.3 |
| RECONSTRUCTION | cryoSPARC | v4.5.3 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 30605819 | Two different types of Csu pilus stack architectures were solved from the same particle set. Particle picking failed to distinguish between the two, so the initial number of particles is the same for both stack architectures. | ||
