6PWB
Rigid body fitting of flagellin FlaB, and flagellar coiling proteins, FcpA and FcpB, into a 10 Angstrom structure of the asymmetric flagellar filament purified from Leptospira biflexa Patoc WT cells resolved via subtomogram averaging
ELECTRON MICROSCOPY
| Sample |
|---|
| Flagellar filament purified from the periplasm of the Spirochete bacterium, Leptospira biflexa |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | FILAMENT |
| Vitrification Instrument | FEI VITROBOT MARK III |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | 2 minute incubation time; blot time of 6-7.5 seconds; and blot offset of -2 mm |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SUBTOMOGRAM AVERAGING |
| Number of Particles | 10581 |
| Reported Resolution (Å) | 9.83 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | emClarity: The two half-dataset volumes were combined with a B-170 factor of 0, and the Gold standard FSC at 0.143 was calculated to be 9.83 A with an ... |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (5WJT, 6NQW, 6NQZ) | ||||
| Refinement Space | RECIPROCAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | Correlation coefficient | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | Eliminate minor clashes between FlaB1, FcpA, and FcpB | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 1.7 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI POLARA 300 |
| Minimum Defocus (nm) | 3000 |
| Maximum Defocus (nm) | 5000 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | SIDE ENTRY, EUCENTRIC |
| Nominal Magnification | 15000 |
| Calibrated Magnification | 19230 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| VOLUME SELECTION | PEET | 1.11 |
| VOLUME SELECTION | RELION | 2.1 |
| IMAGE ACQUISITION | SerialEM | 3 |
| CTF CORRECTION | IMOD | 4.9.4_RHEL6-64_CUDA8.0 |
| CTF CORRECTION | RELION | 2.1.b1-gcccuda-2016.10-cc37 |
| CTF CORRECTION | emClarity | 1..0 |
| MODEL FITTING | Rosetta | 3 |
| MODEL FITTING | Situs | 2.8-foss-2016b |
| MODEL FITTING | UCSF Chimera | 1.12 |
| FINAL EULER ASSIGNMENT | RELION | 2.1.b1-gcccuda-2016.10-cc37 |
| FINAL EULER ASSIGNMENT | emClarity | 1.0 |
| RECONSTRUCTION | emClarity | 1.1 |
| MODEL REFINEMENT | Rosetta | 3 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | CTF estimation was initially done in IMOD. | |||
