ELECTRON MICROSCOPY

Sample

Mycoplasma pneumoniae M129 cells treated with chloramphenicol

Specimen Preperation
Sample Aggregation State CELL
Vitrification Instrument HOMEMADE PLUNGER
Cryogen Name ETHANE-PROPANE
Sample Vitrification Details Back-side blotting for 2-3 seconds before plunging using a manual plunger without an environmental control chamber.
3D Reconstruction
Reconstruction Method SUBTOMOGRAM AVERAGING
Number of Particles 30774
Reported Resolution (Å) 3.2
Resolution Method FSC 0.143 CUT-OFF
Other Details half maps from Warp/M
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol RIGID BODY FIT
Refinement Target Cross-correlation coefficient
Overall B Value ?
Fitting Procedure ?
Details ?
Data Acquisition
Detector Type GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å2) 3.34
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TITAN KRIOS
Minimum Defocus (nm) 1000
Maximum Defocus (nm) 3250
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 64000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
VOLUME SELECTION PyTom 0.9.7.1
VOLUME SELECTION Warp 1.0.9
IMAGE ACQUISITION SerialEM 3.9
CTF CORRECTION Warp 1.0.9
MODEL FITTING Coot 0.9.8.5
FINAL EULER ASSIGNMENT RELION 3.0.8
FINAL EULER ASSIGNMENT Warp 1.0.9
CLASSIFICATION RELION 3.0.8
RECONSTRUCTION Warp 1.0.9
MODEL REFINEMENT PHENIX 1.20.1_4487
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION CTF estimation and 3D CTF correction are done in Warp