Cryo-EM structure of lipid-bound human myoferlin (25 mol% DOPS/5 mol% PI(4,5)P2 nanodisc)
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 5.6588 |
| f_angle_d | 0.7902 |
| f_chiral_restr | 0.0498 |
| f_plane_restr | 0.0069 |
| f_bond_d | 0.0036 |
| Sample |
|---|
| Soluble human myoferlin (residues 1-1997) bound to an MSP2N2-based lipid nanodisc (comprising 25 mol% DOPS and 5 mol% PI(4,5)P2) |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE-PROPANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 233637 |
| Reported Resolution (Å) | 2.56 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | OTHER | ||||
| Refinement Target | |||||
| Overall B Value | 152.37 | ||||
| Fitting Procedure | |||||
| Details | Iterative model building and refinement with ISOLDE, Coot, and Phenix (phenix.real_space_refine) | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON IV (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 39.595 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 800 |
| Maximum Defocus (nm) | 2300 |
| 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 |
| PARTICLE SELECTION | cryoSPARC | v4.5 |
| IMAGE ACQUISITION | EPU | v3.6.0 |
| CTF CORRECTION | cryoSPARC | v4.5 |
| MODEL FITTING | UCSF ChimeraX | v1.8 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | v4.5 |
| FINAL EULER ASSIGNMENT | cryoSPARC | v4.5 |
| CLASSIFICATION | RELION | v5.0 |
| RECONSTRUCTION | cryoSPARC | v4.5 |
| MODEL REFINEMENT | PHENIX | 1.21.2_5419 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 7651843 | |||
