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Cryo-EM structure of Enterotoxigenic Escherichia coli autotransporter A (EatA) complexed with the fragment antigen binding domain of monoclonal antibody G12
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s)
Type
Source
Accession Code
Details
in silico model
AlphaFold
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
4.6993
f_angle_d
0.6956
f_chiral_restr
0.0509
f_plane_restr
0.0065
f_bond_d
0.0032
Sample
Binary complex of the recombinant EatA passenger domain with Fab G12
Sample Components
Enterotoxigenic Escherichia coli autotransporter A (EatA) passenger domain
Fragment antigen binding domain of monoclonal antibody G12
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
Added 1X Lauryl Maltose Neopentyl Glycol (LMNG) detergent to sample prior to vitrification.
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
73337
Reported Resolution (Å)
3.7
Resolution Method
OTHER
Other Details
Estimated resolution of composite map.
Refinement Type
Symmetry Type
POINT
Point Symmetry
C1
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
FLEXIBLE FIT
Refinement Target
Cross-correlation coefficient
Overall B Value
Fitting Procedure
Details
Rigid body fitting of AlphaFold-derived models was done in ChimeraX, followed by multiple rounds of local fitting in Coot and Phenix real-space refine ...
Rigid body fitting of AlphaFold-derived models was done in ChimeraX, followed by multiple rounds of local fitting in Coot and Phenix real-space refinement
Data Acquisition
Detector Type
GATAN K3 BIOCONTINUUM (6k x 4k)
Electron Dose (electrons/Å**2)
49
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
TFS KRIOS
Minimum Defocus (nm)
1000
Maximum Defocus (nm)
2400
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
2.7
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
105000
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
EM Software
Task
Software Package
Version
PARTICLE SELECTION
cryoSPARC
4.7.1
IMAGE ACQUISITION
SerialEM
4
CTF CORRECTION
cryoSPARC
4.7.1
MODEL FITTING
UCSF ChimeraX
1.8
MODEL FITTING
Coot
0.9.8.7
INITIAL EULER ASSIGNMENT
cryoSPARC
4.7.1
FINAL EULER ASSIGNMENT
cryoSPARC
4.7.1
RECONSTRUCTION
cryoSPARC
4.7.1
MODEL REFINEMENT
PHENIX
1.21_5207
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
1244157
Initial particle set was obtained by CryoSegNet AI picking, followed by cryoSPARC 2D classification to redo particle picking with 2D templates