6Y7S
2.85 A cryo-EM structure of the in vivo assembled type 1 pilus rod
ELECTRON MICROSCOPY
Data Collection
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 15.8359 |
| f_angle_d | 0.7424 |
| f_chiral_restr | 0.048 |
| f_bond_d | 0.0048 |
| f_plane_restr | 0.0038 |
| Sample |
|---|
| Type 1 pilus rod |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | FILAMENT |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | 3 ul sample, 30 s wait time, 0.5 s drain time, 6 s blotting |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | HELICAL |
| Number of Particles | 40805 |
| Reported Resolution (Å) | 2.85 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | local searches 0.9 degree with mask |
| Refinement Type | |
| Symmetry Type | HELICAL |
| Axial Symmetry | C1 |
| Axial Rise | 7.85334 |
| Angular Rotation | 115.001 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (5OH0) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | Correlation coefficient | ||||
| Overall B Value | 49.9714 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 50.4 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 1500 |
| Maximum Defocus (nm) | 3500 |
| 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 |
| IMAGE ACQUISITION | EPU | |
| CTF CORRECTION | Gctf | 1.06 |
| MODEL FITTING | UCSF Chimera | |
| MODEL REFINEMENT | PHENIX | |
| INITIAL EULER ASSIGNMENT | RELION | 3.08 |
| FINAL EULER ASSIGNMENT | RELION | 3.08 |
| CLASSIFICATION | RELION | 3.08 |
| RECONSTRUCTION | RELION | 3.08 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 516000 | Autopicking based on the 2D classes from manually chosen filaments | ||
