8BQE
In situ structure of the Caulobacter crescentus S-layer
ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 3.063 |
f_angle_d | 0.281 |
f_chiral_restr | 0.031 |
f_bond_d | 0.001 |
f_plane_restr | 0.001 |
Sample |
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Caulobacter crescentus S-layer |
Specimen Preparation | |
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Sample Aggregation State | CELL |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details | 1.5 s blot |
3D Reconstruction | |
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Reconstruction Method | SUBTOMOGRAM AVERAGING |
Number of Particles | 42990 |
Reported Resolution (Å) | 3.5 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C6 |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 | ||||
Refinement Space | REAL | ||||
Refinement Protocol | RIGID BODY FIT | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
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Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 3.4 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 2000 |
Maximum Defocus (nm) | 5000 |
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 |
EM Software | ||
---|---|---|
Task | Software Package | Version |
VOLUME SELECTION | RELION | 4.0.0 |
IMAGE ACQUISITION | SerialEM | |
CTF CORRECTION | RELION | 4.0.0 |
MODEL FITTING | PHENIX | 1.19-4092 |
MODEL REFINEMENT | PHENIX | 1.19-4092 |
FINAL EULER ASSIGNMENT | RELION | 4.0.0 |
CLASSIFICATION | RELION | 4.0.0 |
RECONSTRUCTION | RELION |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | PseudoSubtomograms as described in Zivanov 2022 (https://www.biorxiv.org/content/10.1101/2022.02.28.482229v2.abstract) |