ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 4V60 | |
| in silico model | AlphaFold | Q9UKK3 | |
| Sample |
|---|
| Ternary complex of NAD+ and human PARP4 bound to oligomerized human MVP |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Vitrification carried out under standard conditions |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 93859 |
| Reported Resolution (Å) | 2.9 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | D39 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (4v60) | 2 | |||
| Refinement Space | REAL | REAL | |||
| Refinement Protocol | FLEXIBLE FIT | FLEXIBLE FIT | |||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | The starting model was the rat homologue of MVP from a previous crystal structure of the vault cage (PDB accession no 4V60). Small molecule coordinate ... | PARP4's MINT domain, predicted by AlphaFold2, was used as the starting model. The final model was refined in real space and validated using PHENIX. | |||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 45 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 700 |
| Maximum Defocus (nm) | 1700 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 0.01 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | 53000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details | Preliminary grid screening was performed manually. |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | 4.4 |
| IMAGE ACQUISITION | SerialEM | 4.0 |
| CTF CORRECTION | cryoSPARC | 4.4 |
| MODEL FITTING | Coot | 0.8.9.2 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 4.4 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 4.4 |
| CLASSIFICATION | cryoSPARC | 4.4 |
| RECONSTRUCTION | cryoSPARC | 4.4 |
| MODEL REFINEMENT | PHENIX | 1.12 |
| MODEL FITTING | Coot | 0.8.9.2 |
| MODEL REFINEMENT | PHENIX | 1.12 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | CTF correction was performed when movies were imported into cryoSPARC Live | 174624 | ||
