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 |
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Flagellar filament purified from the periplasm of the Spirochete bacterium, Leptospira biflexa |
Specimen Preparation | |
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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 | |
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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 | |||||
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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 | |||||||||
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Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 1.7 |
Imaging Experiment | 1 |
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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 | ||
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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 | ||||
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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. |