6SGY

Structure of EccB3 dimer from the ESX-3 core complex

ELECTRON MICROSCOPY

Sample
EccB3 dimeric structure from ESX-3/Type VII secretion system

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	Blotting time: 3s Blotting force: -10

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	55342
Reported Resolution (Å)	4.6
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Particles were extracted centred at extracellular density instead than in the centre of mass in order to improve the resolution in that distal region. ...	Particles were extracted centred at extracellular density instead than in the centre of mass in order to improve the resolution in that distal region. Extra density not corresponding to the EccB3 dimer was subtracted
Refinement Type
Symmetry Type	POINT
Point Symmetry	C2

Map-Model Fitting and Refinement
Id	1 (3X3M)
Refinement Space	REAL
Refinement Protocol	AB INITIO MODEL
Refinement Target	Map correlation coefficient
Overall B Value
Fitting Procedure
Details	Two copies of the periplasmic domain of a EccB3 homology model (based on pdb 3X3M) were fitted into the density and then morphing was performed using ...	Two copies of the periplasmic domain of a EccB3 homology model (based on pdb 3X3M) were fitted into the density and then morphing was performed using PHENIX Real-Space Refinement.

Data Acquisition
Detector Type	FEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)	50

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1600
Maximum Defocus (nm)	2600
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	75000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	RELION
IMAGE ACQUISITION	EPU
CTF CORRECTION	Gctf
MODEL FITTING	PHENIX	1.14
INITIAL EULER ASSIGNMENT	RELION
FINAL EULER ASSIGNMENT	RELION
CLASSIFICATION	RELION
RECONSTRUCTION	RELION
MODEL REFINEMENT	PHENIX	1.14
MODEL REFINEMENT	UCSF Chimera

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		2066007

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 R01GM133198.