ELECTRON MICROSCOPY

Sample

lid-locked beta-barrel assembly machinery (BAM) complex (BamABCDE) bound by a bactericidal Fab fragment

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 61777
Reported Resolution (Å) 7.1
Resolution Method FSC 0.143 CUT-OFF
Other Details Half maps from non-uniform refinement in cryoSPARC were postprocessed in RELION 3.0 to generate the final map
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol FLEXIBLE FIT
Refinement Target ?
Overall B Value 183
Fitting Procedure ?
Details 7NBX (lateral-open BAM-LL cryoEM structure) and 7BM5 (Fab1 crystal structure) were rigid fitted into the electron density in UCSF Chimera. One round of molecular dynamics based flexible fitting was then set up in VMD and run in NAMD to fit the structures into the BAM-LL-Fab1 density. The resulting structure was finally real-space refined in phenix to generate the final model.
Data Acquisition
Detector Type GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å2) 49.1
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TITAN KRIOS
Minimum Defocus (nm) 1000
Maximum Defocus (nm) 2500
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 1.4.1
IMAGE ACQUISITION EPU ?
CTF CORRECTION Gctf 1.18
MODEL FITTING UCSF Chimera ?
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 MDFF ?
MODEL REFINEMENT VMD ?
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 ?