8FAI
Cryo-EM structure of the Agrobacterium T-pilus
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 15.129 |
| f_angle_d | 0.572 |
| f_chiral_restr | 0.034 |
| f_bond_d | 0.003 |
| f_plane_restr | 0.003 |
| Sample |
|---|
| T-pilus |
| Sample Components |
| VirB2 |
| Phosphatidylglycerol 16:1/18:1 |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | FILAMENT |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE-PROPANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | HELICAL |
| Number of Particles | 3543 |
| Reported Resolution (Å) | 3 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | HELICAL |
| Axial Symmetry | C5 |
| Axial Rise | 13.44 |
| Angular Rotation | 32.62 |
| Axial Symmetry | C1 |
| Axial Rise | 13.44 |
| Angular Rotation | 32.62 |
| Axial Symmetry | C1 |
| Axial Rise | 13.44 |
| Angular Rotation | 32.62 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | |||||
| Refinement Protocol | |||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 60 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 700 |
| Maximum Defocus (nm) | 2000 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.7 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | 105000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | RELION | 4.0beta2 |
| IMAGE ACQUISITION | SerialEM | 3-9-0beta7 |
| CTF CORRECTION | RELION | 4.0beta2 |
| MODEL FITTING | Rosetta | 3 |
| MODEL REFINEMENT | PHENIX | 1.19.2 |
| INITIAL EULER ASSIGNMENT | RELION | 4.0beta2 |
| FINAL EULER ASSIGNMENT | RELION | 4.0beta2 |
| CLASSIFICATION | RELION | 4.0beta2 |
| RECONSTRUCTION | RELION | 4.0beta2 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 10934 | Filaments were manually picked using EMAN2 e2helixboxer and particles were extracted by RELION. | ||
