ELECTRON MICROSCOPY

Sample

Structure of hexameric S-layer protein csg

Specimen Preperation
Sample Aggregation State 2D ARRAY
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details Vitrobot options: Blot time 4.5 seconds, Blot force -10,1, Wait time 10 seconds, Drain time 0.5 seconds
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 1087798
Reported Resolution (Å) 3.46
Resolution Method FSC 0.143 CUT-OFF
Other Details Particles from classes with the same curvature were combined, re-extracted in 400 x 400 boxes and subjected to a focused 3D auto refinement on the central 6 subunits using the scaled and lowpass filtered output from the 3D classification as a starting model. 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 (Zivanov et al., 2020).
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol AB INITIO MODEL
Refinement Target Best Fit
Overall B Value 143.26
Fitting Procedure ?
Details The boundaries of the six Ig-like domains, D1-D6, were predicted using HHpred (Steinegger et al., 2019) in default settings within the MPI Bioinformatics Toolkit (Zimmermann et al., 2018). Subsequently, structural models for these domains were built using the Robetta structure prediction server, employing the deep learning-based modelling method TrRosetta (Yang et al., 2020). The obtained structural models of domains D3-D6 resulted in an overall fit into the hexameric cryo-EM map of csg from the reconstituted sheets. D1-D2 deviated significantly from any obtained homology models, and for those domains, the carbon backbone of the csg protein was manually traced through a single subunit of the hexameric cryo-EM density using Coot (Emsley and Cowtan, 2004). Due to the edge effect of the box used in the refinement of the 3.5 angstrom map, parts of D6 displayed edge artefacts. These artefacts were removed using single-particle cryo-EM refinement in a larger box, which led to an overall slightly lower resolution (3.8 angstrom) but allowed fitting of the D6 homology model unambiguously. Following initial manual building (for D1-D2) or fitting in of structural models (for D3-D6), side chains were assigned in regions with density corresponding to characteristic aromatic residues allowing us to deduce the register of the amino acid sequence in the map. Another important check of the model building was the position of known glycan positions, which were readily assigned based on large unexplained densities on characteristic asparagine residues. The atomic model was then placed into the hexameric map in six copies and subjected to several rounds of refinement using refmac5 (Murshudov et al., 2011) inside the CCP-EM software suite (Burnley et al., 2017) and PHENIX (Liebschner et al., 2019), followed by manually rebuilding in Coot (Emsley and Cowtan, 2004). Model validation was performed in PHENIX and CCP-EM.
Data Acquisition
Detector Type GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å2) 51.441
Imaging Experiment
Date of Experiment ?
Temprature (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 81000
Calibrated Magnification 81000
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details EPU software with faster acquisition mode AFIS (Aberration Free Image Shift).
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION Topaz 0.2.5
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 PHENIX 1.19-4092
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.