9CMW | pdb_00009cmw

The cryo-EM structure of BamACDE complex from Neisseria gonorrhoeae

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4K3B
experimental model	PDB	5WAQ
experimental model	PDB	5WAM

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.103
f_angle_d	0.545
f_chiral_restr	0.04
f_plane_restr	0.003
f_bond_d	0.002

Sample
NgBamACDE

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	Blot force of 2, blot time of 15 seconds.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	95431
Reported Resolution (Å)	4
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (4K3B, 5WAQ, 5WAM)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	41.87

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	2230
Maximum Defocus (nm)	9700
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	81000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	3.2
IMAGE ACQUISITION	Leginon
CTF CORRECTION	cryoSPARC	3.2
MODEL FITTING	UCSF ChimeraX
CLASSIFICATION	cryoSPARC	3.2
RECONSTRUCTION	cryoSPARC	3.2
MODEL REFINEMENT	PHENIX

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		4552267