7NCS

Lateral-open conformation of the lid-locked BAM complex (BamA E435C S665C, BamBDCE) bound by a bactericidal Fab fragment

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7NBX
experimental model	PDB	7BM5

Sample
lid-locked beta-barrel assembly machinery (BAM) complex (BamABCDE) bound by a bactericidal Fab fragment
Sample Components
lid-locked beta-barrel assembly machinery (BAM) complex (BamABCDE)
Light and heavy chains of bactericidal Fab fragment Fab1

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	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 (7NBX, 7NBX, 7NBX, 7NBX, 7NBX, 7BM5, 7BM5)
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 ...	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/Å**2)	49.1

Imaging Experiment	1
Date of Experiment
Temperature (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

EM Software
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		162844

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.