ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 3.636 |
| f_angle_d | 0.388 |
| f_chiral_restr | 0.056 |
| f_bond_d | 0.009 |
| f_plane_restr | 0.002 |
| Sample |
|---|
| uperin 3.5 |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | FILAMENT |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE-PROPANE |
| Sample Vitrification Details | wait time 15s after application, blot time 4s |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | HELICAL |
| Number of Particles | 215020 |
| Reported Resolution (Å) | 3 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | HELICAL |
| Axial Symmetry | C3 |
| Axial Rise | 4.86 |
| Angular Rotation | -1.14 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | CC | ||||
| Overall B Value | 59.34 | ||||
| Fitting Procedure | |||||
| Details | - Initial model building of a single helical layer using ChimeraX and Coot - Expansion to three layers, refinement in ISOLDE - Truncation of outer lay ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 40 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 500 |
| 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 | crYOLO | 1.8-beta |
| IMAGE ACQUISITION | EPU | 2.8.0.1256 |
| IMAGE ACQUISITION | DigitalMicrograph | 3.32.2403 |
| CTF CORRECTION | RELION | 3.1.3 |
| MODEL FITTING | UCSF ChimeraX | 1.3 |
| MODEL FITTING | Coot | 0.9.3 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 2.3 |
| INITIAL EULER ASSIGNMENT | RELION | 3.1.3 |
| FINAL EULER ASSIGNMENT | RELION | 3.1.3 |
| CLASSIFICATION | RELION | 3.1.3 |
| RECONSTRUCTION | RELION | 3.1.3 |
| MODEL REFINEMENT | PHENIX | 1.19.1 |
| MODEL REFINEMENT | ISOLDE | 1.0 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | CTF refined after 3D reconstruction | 2447463 | 4 unique helical units per segment | |
