9Z7B | pdb_00009z7b

Cryo-EM structure of Protein involved in colonization (Pic) from Enteroaggregative Escherichia coli complexed with the fragment antigen binding domain of monoclonal antibody 40

ELECTRON MICROSCOPY

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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	4.8294
f_angle_d	0.6685
f_chiral_restr	0.05
f_plane_restr	0.0065
f_bond_d	0.0034

Sample
Binary complex of the recombinant Pic passenger domain with Fab 40
Sample Components
Protein involved in colonization (Pic) from Enteroaggregative Escherichia coli passenger domain
Fragment antigen binding domain of monoclonal antibody 40

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	127391
Reported Resolution (Å)	2.69
Resolution Method	FSC 0.143 CUT-OFF
Other Details
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 refinement

Data Acquisition
Detector Type	TFS FALCON 4i (4k x 4k)
Electron Dose (electrons/Å**2)	41

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	800
Maximum Defocus (nm)	2200
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	130000
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	EPU
CTF CORRECTION	cryoSPARC	4.7.1
MODEL FITTING	UCSF ChimeraX	1.8
MODEL FITTING	Coot	0.9.8.7
MODEL REFINEMENT	PHENIX	1.21.2_5419
INITIAL EULER ASSIGNMENT	cryoSPARC	4.7.1
FINAL EULER ASSIGNMENT	cryoSPARC	4.7.1
RECONSTRUCTION	cryoSPARC	4.7.1

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		1071006	Initial particle set was obtained by CryoSegNet AI picking, followed by cryoSPARC 2D classification to redo particle picking with 2D templates