ELECTRON MICROSCOPY


Sample

beta-barrel assembly machinery (BAM) complex (BamABCDE)

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details ?
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 141612
Reported Resolution (Å) 4.8
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 FLEXIBLE FIT
Refinement Target ?
Overall B Value 211
Fitting Procedure ?
Details Initial local fitting accomplished in Chimera. VMD was then used to setup cMDFF simulations that were run using NAMD. Both 7BNQ and 5LJO were used as initial models, with the best fitting parts of each then combined and flexibly fit again to generate the final conformation. This was then Real Space Refined in Phenix to generate the final structure
Data Acquisition
Detector Type GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å2) 49.7
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TITAN KRIOS
Minimum Defocus (nm) 1500
Maximum Defocus (nm) 3000
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 130000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION crYOLO 1.3.5
IMAGE ACQUISITION EPU ?
CTF CORRECTION Gctf 1.18
MODEL FITTING UCSF Chimera ?
MODEL FITTING VMD ?
INITIAL EULER ASSIGNMENT RELION 3.0
FINAL EULER ASSIGNMENT cryoSPARC 2.2.0
CLASSIFICATION RELION 3.0
RECONSTRUCTION RELION 3.0
RECONSTRUCTION cryoSPARC 2.2.0
MODEL REFINEMENT NAMD ?
MODEL REFINEMENT PHENIX 1.14
MODEL REFINEMENT Coot 0.9
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?