7PTT
In-situ structure of hexameric S-layer protein
ELECTRON MICROSCOPY
Sample |
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In-situ structure of hexameric S-layer of Haloferax volcanii |
Specimen Preparation | |
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Sample Aggregation State | CELL |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details | Vitrobot options: Blot time 2.0 seconds, Blot force -15,1, Wait time 0 seconds, Drain time 0.5 seconds |
3D Reconstruction | |
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Reconstruction Method | SUBTOMOGRAM AVERAGING |
Number of Particles | 53063 |
Reported Resolution (Å) | 7.968 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C6 |
Map-Model Fitting and Refinement | |||||
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Id | 1 | ||||
Refinement Space | REAL | ||||
Refinement Protocol | RIGID BODY FIT | ||||
Refinement Target | Best Fit | ||||
Overall B Value | |||||
Fitting Procedure | |||||
Details | Rigid body fit inside coot of D1-D6 domains and real space refinement with restraints of the original model obtained by single particle analysis in PH ... |
Data Acquisition | |||||||||
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Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 2.9 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 1000 |
Maximum Defocus (nm) | 4000 |
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 | 105000 |
Calibrated Magnification | 105000 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details | SerialEM Hagen Scheme |
EM Software | ||
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Task | Software Package | Version |
VOLUME SELECTION | RELION | 3.1 |
IMAGE ACQUISITION | SerialEM | |
CTF CORRECTION | CTFFIND | 4.1.13 |
MODEL FITTING | Coot | 0.9.2-pre |
INITIAL EULER ASSIGNMENT | RELION | 3.0 |
FINAL EULER ASSIGNMENT | RELION | 3.1 |
CLASSIFICATION | RELION | 3.1 |
RECONSTRUCTION | RELION | 3.1 |
MODEL REFINEMENT | PHENIX | 1.19-4092 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | RELION subtomogram averaging (Bharat & Scheres 2016) | 1773652 | Particles were initially picking using the Laplacian-of gaussian algorithm implemented in RELION3.0 (Zivanov et al., 2018). Particles were extracted in 8x down-sampled in 50x50 pixel boxes and classified using reference-free 2D classification inside RELION3.0. |