Experiment: 7NBX

Lateral-open conformation of the lid-locked BAM complex (BamA E435C S665C, BamBDCE) by cryoEM

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7BNQ
experimental model	PDB	5LJO

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

Specimen Preparation
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 (7BNQ, 7BNQ, 5LJO, 5LJO, 7BNQ, 7BNQ, 7BNQ, 7BNQ)
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 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/Å**2)	49.7

Imaging Experiment	1
Date of Experiment
Temperature (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

EM Software
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		793444