ELECTRON MICROSCOPY
| Sample |
|---|
| AlbAB cyclodipeptide oxidase enzyme filament |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | FILAMENT |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Grid was plunge frozen into liquid ethane using the following parameters: blot force- 5, blot time 2 seconds |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | HELICAL |
| Number of Particles | 795765 |
| Reported Resolution (Å) | 2.78 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Final reconstruction was generated by a masked local refinement of the helically refined map. The mask encompassed one dimer of AlbA and two surroundi ... |
| Refinement Type | |
| Symmetry Type | HELICAL |
| Axial Symmetry | C1 |
| Axial Rise | 46.063 |
| Angular Rotation | 119.969 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | Cross-correlation coefficient | ||||
| Overall B Value | 107.4 | ||||
| Fitting Procedure | |||||
| Details | A model of AlbAB was created using AlphaFold2 using MMseqs2 via ColabFold. The model was then fit into the cryoEM density using ChimeraX. The model wa ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 50.12 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 1000 |
| Maximum Defocus (nm) | 2500 |
| 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 | 4.2.1 |
| IMAGE ACQUISITION | SerialEM | |
| CTF CORRECTION | cryoSPARC | 4.2.1 |
| MODEL FITTING | UCSF ChimeraX | 1.5 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 4.2.1 |
| RECONSTRUCTION | cryoSPARC | 4.2.1 |
| MODEL REFINEMENT | PHENIX | 1.20.1-4487 |
| MODEL REFINEMENT | Coot | 0.9.8.1 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 1202923 | |||
