8AE1
Structure of trimeric SlpA outer membrane protein
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 3.918 |
| f_angle_d | 0.453 |
| f_chiral_restr | 0.043 |
| f_plane_restr | 0.003 |
| f_bond_d | 0.002 |
| Sample |
|---|
| Structure of trimeric SlpA protein |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Vitrobot options: Blot time 4.5 seconds, Blot force -10,1, Wait time 10 seconds, Drain time 0.5 seconds |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 122412 |
| Reported Resolution (Å) | 3.25 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C3 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | AB INITIO MODEL | ||||
| Refinement Target | Best Fit | ||||
| Overall B Value | 51.67 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 47.909 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 1000 |
| Maximum Defocus (nm) | 4000 |
| 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 | 81000 |
| Calibrated Magnification | 81000 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details | EPU software with faster acquisition mode AFIS (Aberration Free Image Shift). |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | Topaz | 0.2.5 |
| IMAGE ACQUISITION | EPU | |
| CTF CORRECTION | CTFFIND | 4.1.13 |
| MODEL FITTING | Coot | 0.9.2-pre |
| MODEL REFINEMENT | PHENIX | 1.19-4092 |
| INITIAL EULER ASSIGNMENT | RELION | 3.1 |
| FINAL EULER ASSIGNMENT | RELION | 3.1 |
| CLASSIFICATION | RELION | 3.1 |
| RECONSTRUCTION | RELION | 3.1 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | RELION refinement with in-built CTF correction. The function is similar to a Wiener filter, so amplitude correction included. | 223878 | Initially, micrographs were denoised using TOPAZ (73) using the UNET neural network and 2893 particles were manually picked. Particle coordinates were used to train TOPAZ picker (74) in 5 times downsampled micrographs with the neural network architecture ResNet8 and picked particles were extracted in 4 times downsampled 128 x 128 boxes and classified using reference-free 2D classification inside RELION3.1. | |
