Cryo-EM structure of the binary MEGF8-MOSMO complex with nanobody 270
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 9QQS | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 6.462 |
| f_angle_d | 0.492 |
| f_chiral_restr | 0.042 |
| f_plane_restr | 0.004 |
| f_bond_d | 0.002 |
| Sample |
|---|
| Human MEGF8-MOSMO binary complex bound to nanobody 270 |
| Sample Components |
| MOSMO |
| MEGF8 |
| Nanobody 270 |
| 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 | 228513 |
| Reported Resolution (Å) | 2.98 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Local refinement with a mask containing MEGF8, MOSMO and nanobody 270 was performed after non-uniform refinement, to mask out the micelle. |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (9QQS) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | |||||
| Overall B Value | 143.4 | ||||
| Fitting Procedure | |||||
| Details | Initial local fitting was done using ChimeraX then manual model building in Coot was interspersed with real space refinement in Phenix. | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | TFS FALCON 4i (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 50 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 1400 |
| Maximum Defocus (nm) | 2600 |
| 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 | 165000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| MODEL REFINEMENT | PHENIX | 1.21rc1_5156: |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | Patch CTF estimation was performed in cryoSPARC live pre-processing. | 2266859 | Template picker using 2D classes from a screening dataset collected on a different grid. | |
