ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 5NUP | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 17.352 |
| f_angle_d | 1.146 |
| f_chiral_restr | 0.066 |
| f_bond_d | 0.006 |
| f_plane_restr | 0.006 |
| Sample |
|---|
| Outer membrane complex of OmpC-MlaA with periplasmic MlaC reconstituted in MSP2N2 nanodiscs |
| Sample Components |
| Outer membrane porin C |
| Intermembrane phospholipid transport system lipoprotein MlaA |
| 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 | 205487 |
| Reported Resolution (Å) | 2.93 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (5NUP, 5NUP, 5NUP, 5NUP) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | Cross-correlation coefficient | ||||
| Overall B Value | 88 | ||||
| Fitting Procedure | |||||
| Details | Building of the high-resolution structures of OmpC-MlaA was done via approximate fitting using the OmpC-MlaA crystal structure (PDB 5NUP) as rigid bod ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 90 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 800 |
| Maximum Defocus (nm) | 2000 |
| 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 | 105000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | 4.0.0 |
| IMAGE ACQUISITION | SerialEM | |
| CTF CORRECTION | cryoSPARC | 4.0.0 |
| MODEL FITTING | UCSF Chimera | 1.15 |
| MODEL FITTING | Coot | 0.9.4.1 EL |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 4.0.0 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 4.0.0 |
| CLASSIFICATION | cryoSPARC | 4.0.0 |
| RECONSTRUCTION | cryoSPARC | 4.0.0 |
| MODEL REFINEMENT | PHENIX | 1.20.1-4487 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | Patch CTF routine in cryoSPARC | 2434319 | We performed automated particle picking using Blob and Template Picker for initial template picking and final sampling respectively. | |
