ELECTRON MICROSCOPY

Sample

Structure of pentameric S-layer protein csg

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details Vitrobot options: Blot time 5 seconds, Blot force -10,1, Wait time 10 seconds, Drain time 0.5 seconds
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 382105
Reported Resolution (Å) 3.87
Resolution Method FSC 0.143 CUT-OFF
Other Details The final map (RELION3.1) was obtained from 382,105 particles and post-processed using a soft mask focused on the entire pentameric map yielding a global resolution of 3.87 angstrom with resolution anisotropy from 3.49-8.11 angstrom from the central C5 axis near domains D1-D3 (well resolved) to the more flexible domains D4 (partially resolved) and D5-D6 (not resolved).
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 179.68
Fitting Procedure ?
Details The initial manual build of D1-D2 was performed independently using the csg pentameric cryo-EM map, which served as an additional validation of the manual building performed in the csg hexamer in the related deposition. The manual building exercise yielded a nearly identical result to the hexamer; thus, the final refined hexameric structures of D1-D2, along with D3-D4 were taken and fitted into the pentameric map (~3.87 angstrom resolution in D1-D3, lower in D4 which is partially resolved). Five copies of these D1-D4 were used for refinement and model building as for the hexamer, except D3 and D4 was restrained in position, due to steadily deteriorating resolution in this part of the map. D5-D6 were not resolved in the pentameric structure and were thus not included in the refinements. Model validation was performed in PHENIX and CCP-EM.
Data Acquisition
Detector Type GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å2) 53.9
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 RELION 3.0
IMAGE ACQUISITION EPU ?
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
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.
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