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Structure of Hexagonally Packed Intermediate-layer (HPI) protein
Specimen Preparation
Sample Aggregation State
2D ARRAY
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
SINGLE PARTICLE
Number of Particles
55345
Reported Resolution (Å)
2.52
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Per-particle defocus, anisotropy magnification, and higher-order aberrations were refined inside RELION3.1, followed by another round of focused 3D au ...
Per-particle defocus, anisotropy magnification, and higher-order aberrations were refined inside RELION3.1, followed by another round of focused 3D auto refinement and Bayesian particle polishing. The final map was obtained from 55,345 particles and post-processed using a soft mask focused on the central hexamer, including the dimeric bridge, yielding a global resolution of 2.52 Angstrom according to the gold standard Fourier shell correlation criterion of 0.143.
Refinement Type
Symmetry Type
POINT
Point Symmetry
C6
Map-Model Fitting and Refinement
Id
1
Refinement Space
RECIPROCAL
Refinement Protocol
AB INITIO MODEL
Refinement Target
Best Fit
Overall B Value
19.48
Fitting Procedure
Details
Data Acquisition
Detector Type
GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)
53.245
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
81000
Calibrated Magnification
81000
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
EM Software
Task
Software Package
Version
PARTICLE SELECTION
Topaz
0.2.5
PARTICLE SELECTION
RELION
3.1.2
IMAGE ACQUISITION
EPU
CTF CORRECTION
CTFFIND
4.1.13
MODEL FITTING
Coot
0.9.2-pre
INITIAL EULER ASSIGNMENT
RELION
3.1
FINAL EULER ASSIGNMENT
RELION
3.1
CLASSIFICATION
RELION
3.1
RECONSTRUCTION
RELION
3.1
MODEL REFINEMENT
REFMAC
5.8.0403
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
RELION refinement with in-built CTF correction. The function is similar to a Wiener filter, so amplitude correction included.
882866
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 40 Angstrom. Top and tilted views were manually picked at the central hexameric axis. Manually picked particles were extracted in 4x downsampled 100 x 100 boxes and classified using reference-free 2D classification inside RELION3.1. Class averages centered at a hexameric axis were used to automatically pick particles inside RELION3.1. Automatically picked particles were extracted in 4x downsampled 100x100 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 RELION3.1, which TOPAZ did not readily identify. Particles were extracted in 4x downsampled 100x100 pixel2 boxes and classified using reference-free 2D classification inside RELION3.1. 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 100x100 pixel2 boxes.