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In situ structure of the Nitrosopumilus maritimus S-layer - Two-fold symmetry (C2)
ELECTRON MICROSCOPY
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
4.263
f_angle_d
0.458
f_chiral_restr
0.043
f_plane_restr
0.003
f_bond_d
0.002
Sample
Nitrosopumilus maritimus S-layer
Specimen Preparation
Sample Aggregation State
CELL
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
NITROGEN
Sample Vitrification Details
absorption for 60 sec and blotted for 5 sec with blot force -10
3D Reconstruction
Reconstruction Method
SUBTOMOGRAM AVERAGING
Number of Particles
108621
Reported Resolution (Å)
3.4
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Point Symmetry
C2
Map-Model Fitting and Refinement
Id
1
Refinement Space
RECIPROCAL
Refinement Protocol
AB INITIO MODEL
Refinement Target
Best Fit
Overall B Value
66.19
Fitting Procedure
Details
Data Acquisition
Detector Type
GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)
2.96
Imaging Experiment
1
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
CTFFIND
4.1.13
CTF CORRECTION
RELION
4.0.0
MODEL FITTING
Coot
0.9.2-pre
MODEL REFINEMENT
PHENIX
1.19-4092
MODEL REFINEMENT
REFMAC
INITIAL EULER ASSIGNMENT
RELION
3.1
FINAL EULER ASSIGNMENT
RELION
4.0.0
CLASSIFICATION
RELION
4.0.0
RECONSTRUCTION
RELION
4.0.0
Image Processing
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://elifesciences.org/articles/83724)
1971908
Initially, side views of S-layer sheets were first manually picked along the edge of the lattice using the helical picking tab in RELION while setting the helical rise to 60 angstrom. Top and tilted views were manually picked at the central hexameric axis. Manually picked particles were extracted in 4x downsampled 128x128 pixel2 boxes and classified using reference-free 2D classification inside RELION-3.1. Class averages centered at a hexameric axis were used to automatically pick particles inside RELION-3.1. Automatically picked particles were extracted in 4x downsampled 128x128 pixel2 boxes and classified using reference-free 2D classification. Particle coordinates belonging to class averages centered at the hexameric axis were used to train TOPAZ in 5x downsampled micrographs with the neural network architecture conv127. For the final reconstruction, particles were picked using TOPAZ and the previously trained neural network above. Additionally, top, bottom, and side views were picked using the reference-based autopicker inside RELION-3.1, which TOPAZ did not readily identify. Particles were extracted in 4x downsampled 128x128 pixel2 boxes and classified using reference-free 2D classification inside RELION-3.1. Particles belonging to class averages centered at the hexameric axis were combined, and particles within 30 angstrom were removed to prevent duplication after alignment. All resulting particles were then re-extracted in 4x downsampled 128x128 pixel2 boxes.