ELECTRON MICROSCOPY

Sample

Nitrosopumilus maritimus S-layer

Specimen Preperation
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
Map-Model Fitting and Refinement
ID 1
Refinement Space RECIPROCAL
Refinement Protocol AB INITIO MODEL
Refinement Target Best Fit
Overall B Value 72.45
Fitting Procedure ?
Details ?
Data Acquisition
Detector Type GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å2) 2.96
Imaging Experiment
Date of Experiment ?
Temprature (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 ?
Imaging Experiment
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
INITIAL EULER ASSIGNMENT RELION 3.1
FINAL EULER ASSIGNMENT RELION 4.0.0
CLASSIFICATION RELION 4.0.0
RECONSTRUCTION RELION 4.0.0
MODEL REFINEMENT PHENIX 1.19-4092
MODEL REFINEMENT REFMAC ?
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)