5VXX
Cryo-EM reconstruction of Neisseria gonorrhoeae Type IV pilus
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 8.562 |
| f_angle_d | 4.37 |
| f_chiral_restr | 0.504 |
| f_bond_d | 0.017 |
| f_plane_restr | 0.007 |
| Sample |
|---|
| Neisseria gonorrhoeae Type IV pilin filament |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | FILAMENT |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | HELICAL |
| Number of Particles | 9855 |
| Reported Resolution (Å) | 5.1 |
| Resolution Method | OTHER |
| Other Details | model-map FSC 0.38 cut-off |
| Refinement Type | |
| Symmetry Type | HELICAL |
| Axial Symmetry | C1 |
| Axial Rise | 10.1 |
| Angular Rotation | 100.8 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | |||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON II (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 20 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | |
| Maximum Defocus (nm) | |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | EMAN2 | |
| IMAGE ACQUISITION | EPU | |
| CTF CORRECTION | CTFFIND3 | |
| MODEL FITTING | Rosetta | |
| MODEL REFINEMENT | PHENIX | |
| MODEL REFINEMENT | Coot | |
| INITIAL EULER ASSIGNMENT | SPIDER | |
| FINAL EULER ASSIGNMENT | SPIDER | |
| CLASSIFICATION | SPIDER | |
| RECONSTRUCTION | SPIDER | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||
