ELECTRON MICROSCOPY

Sample

Thermoplasma acidophilum 20S proteasome

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument HOMEMADE PLUNGER
Cryogen Name ETHANE
Sample Vitrification Details 3 uL of sample/grid was manually blotted for 4 seconds prior to immediate plunge-freezing in liquid nitrogen-cooled ethane.
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 106581
Reported Resolution (Å) 3.1
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 OTHER
Refinement Target Maximum Likelihood
Overall B Value 101
Fitting Procedure ?
Details Starting model was generated by stripping PDB entry 1YAR of all ligands and alternate conformations, then refining into the EM density using imposed symmetry while adjusting weighting/scoring according to estimated map resolution. The top 10 generated models (ranked based on quality metrics) were real-space refined using Phenix software.
Data Acquisition
Detector Type GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å2) 65
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TALOS ARCTICA
Minimum Defocus (nm) 800
Maximum Defocus (nm) 2800
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 45000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 200
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION FindEM ?
IMAGE ACQUISITION Leginon 3.2
CTF CORRECTION CTFFIND 4
CTF CORRECTION Gctf 1.06
CTF CORRECTION RELION 1.4
MODEL FITTING Rosetta 2016.32.5883
MODEL REFINEMENT PHENIX 1.11.1-2580
INITIAL EULER ASSIGNMENT RELION 2.0
FINAL EULER ASSIGNMENT RELION 2.0
RECONSTRUCTION RELION 2.0
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?