Open state without NUQM and without flavoprotein (classification state 4) of Pichia pastoris mitochondrial complex I in cMSP26 nanodiscs
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | XXXX | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 13.0766 |
| f_angle_d | 0.4991 |
| f_chiral_restr | 0.0411 |
| f_bond_d | 0.0044 |
| f_plane_restr | 0.0039 |
| Sample |
|---|
| Pichia Pastoris (Komagataella phaffi) mitochondrial complex I (NADH:ubiquinone oxidoreductase) |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK III |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | 2s blot time and -10 blot force |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 18608 |
| Reported Resolution (Å) | 3.8 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (9ihr) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | |||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | The initial model was built into a map using ModelAngelo in RELION v5.0 to generate state 1. This model then had the required subunits deleted, and th ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | TFS FALCON 4i (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 47.79 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 600 |
| Maximum Defocus (nm) | 1800 |
| 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 | 130000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | RELION | 4.0 |
| PARTICLE SELECTION | Topaz | |
| IMAGE ACQUISITION | EPU | 3.6.0.6389 |
| CTF CORRECTION | RELION | 4.0 |
| MODEL FITTING | Coot | 0.9.8.92 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 3.3 |
| FINAL EULER ASSIGNMENT | RELION | 4.0 |
| CLASSIFICATION | RELION | 4.0 |
| RECONSTRUCTION | RELION | 4.0 |
| MODEL REFINEMENT | PHENIX | 1.21_5207 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING ONLY | 1350752 | |||
