ELECTRON MICROSCOPY

Sample

In-situ structure of pentameric S-layer of Haloferax volcanii

Specimen Preperation
Sample Aggregation State CELL
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details Vitrobot options: Blot time 2.0 seconds, Blot force -15,1, Wait time 0 seconds, Drain time 0.5 seconds
3D Reconstruction
Reconstruction Method SUBTOMOGRAM AVERAGING
Number of Particles 1640
Reported Resolution (Å) 11.58
Resolution Method FSC 0.143 CUT-OFF
Other Details ?
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol RIGID BODY FIT
Refinement Target Best Fit
Overall B Value ?
Fitting Procedure ?
Details Rigid body fit inside coot of D1-D6 domains and real space refinement with restraints of the original model obtained by single particle analysis in PHENIX.
Data Acquisition
Detector Type GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å2) 2.9
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 105000
Calibrated Magnification 105000
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details SerialEM Hagen Scheme
Imaging Experiment
Task Software Package Version
VOLUME SELECTION RELION 3.1
IMAGE ACQUISITION SerialEM ?
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 subtomogram averaging (Bharat & Scheres 2016)