Experiment: 7K7H

Density-fitted Model Structure of Antibody Variable Domains of TyTx1 in Complex with PltB pentamer of Typhoid Toxin

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4RHR
experimental model	PDB	1MHH
experimental model	PDB	4H20

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	3.668
f_angle_d	0.503
f_chiral_restr	0.042
f_bond_d	0.003
f_plane_restr	0.003

Sample
Complex of TyTx1 Fab with Typhoid toxin
Sample Components
Typhoid toxin
TyTx1 Fab

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	blot for 2.5 second before plunging

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	326766
Reported Resolution (Å)	3
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (4RHR, 1MHH, 4H20)
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details	Initial local fitting was done using Chimera and then Coot was used for rebuilding Fab variable domains into correct sequences. Refinement was perform ...	Initial local fitting was done using Chimera and then Coot was used for rebuilding Fab variable domains into correct sequences. Refinement was performed using Real Space Refine in PHENIX and was iterated with manual building in Coot.

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	53

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TALOS ARCTICA
Minimum Defocus (nm)	800
Maximum Defocus (nm)	1500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	49000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
IMAGE ACQUISITION	SerialEM
CTF CORRECTION	Gctf
MODEL FITTING	Coot	0.8.9.1
MODEL REFINEMENT	PHENIX	1.16-3549
RECONSTRUCTION	RELION	3

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