Cryo-EM structure of Secreted extracellular protein A (SepA) from Shigella flexneri complexed with the fragment antigen binding domain of monoclonal antibody 40
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 5.6725 |
| f_angle_d | 0.7296 |
| f_chiral_restr | 0.0502 |
| f_plane_restr | 0.0056 |
| f_bond_d | 0.0047 |
| Sample |
|---|
| Binary complex of the recombinant SepA passenger domain with Fab 40 |
| Sample Components |
| Secreted extracellular protein A (SepA) from Shigella flexneri passenger domain |
| Fragment antigen binding domain of monoclonal antibody 40 |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Added 1X Lauryl Maltose Neopentyl Glycol (LMNG) detergent to sample prior to vitrification. |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 663017 |
| Reported Resolution (Å) | 1.99 |
| 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 | FLEXIBLE FIT | ||||
| Refinement Target | Cross-correlation coefficient | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | Rigid body fitting of AlphaFold-derived models was done in ChimeraX, followed by multiple rounds of local fitting in Coot and Phenix real-space refine ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | TFS FALCON 4i (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 41 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 800 |
| Maximum Defocus (nm) | 2200 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.7 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | 130000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | 4.7.1 |
| IMAGE ACQUISITION | EPU | |
| CTF CORRECTION | cryoSPARC | 4.7.1 |
| MODEL FITTING | UCSF ChimeraX | 1.8 |
| MODEL FITTING | Coot | 0.9.8.7 |
| MODEL REFINEMENT | PHENIX | 1.21.2_5419 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 4.7.1 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 4.7.1 |
| RECONSTRUCTION | cryoSPARC | 4.7.1 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 2865944 | Initial particle set was obtained by CryoSegNet AI picking, followed by cryoSPARC 2D classification to redo particle picking with 2D templates | ||
