Single particle cryo-EM structure of human MTCH2
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| in silico model | AlphaFold | ||
| experimental model | PDB | 8HBV | |
| Sample |
|---|
| MTCH2 complexed with UCP1 nanobody |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 485622 |
| Reported Resolution (Å) | 3.6 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Final map generated by local refinement in cryoSPARC using a soft mask encompassing MTCH2 only. |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (8HBV) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | Real-space correlation coefficient | ||||
| Overall B Value | 136 | ||||
| Fitting Procedure | |||||
| Details | Initial fitting was done using Coot and refined by Phenix cryo-EM real space refinement. | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 60 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 800 |
| Maximum Defocus (nm) | 1800 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.6 |
| 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 | 4.7.0 |
| IMAGE ACQUISITION | SerialEM | |
| CTF CORRECTION | cryoSPARC | 4.7.0 |
| MODEL FITTING | Coot | 0.9.8.95 |
| MODEL REFINEMENT | PHENIX | 1.21.2_5419 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 4.7.0 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 4.7.0 |
| CLASSIFICATION | cryoSPARC | 4.7.0 |
| RECONSTRUCTION | cryoSPARC | 4.7.0 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | CTF parameters estimated using Patch CTF estimation in cryoSPARC. Global CTF correction for beam tilt was additionally performed. | 4791546 | 14,190 out of 15,334 micrographs were selected for downstream processing. A total of 4,791,546 particles from blob picker and template picker were obtained. After running 11 rounds of heterogenous refinement, 485,622 particles were selected for further processing. | |
