9GO9 | pdb_00009go9

Prepore state of alpha-Latrotoxin

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	3.8218
f_angle_d	0.5201
f_chiral_restr	0.0388
f_plane_restr	0.0043
f_bond_d	0.0021

Sample
tetrameric complex of alpha-latrotoxin

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK II
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	442105
Reported Resolution (Å)	2.7
Resolution Method	FSC 0.143 CUT-OFF
Other Details	For the final reconstruction, Multibody-refinement, as implemented in Relion was performed, with a total of 8 independent bodies.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	AB INITIO MODEL
Refinement Target	cross correlation 0.72
Overall B Value	116
Fitting Procedure
Details	An Alphafold2 prediction was initially fit into the reconstructiuon using ChimeraX and then manually refined using Coot and energy minimized using Phenix.

Data Acquisition
Detector Type	TFS FALCON 4i (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)	300
Maximum Defocus (nm)	1700
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	215000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	crYOLO	1.8.3
IMAGE ACQUISITION	EPU	3.2.0.4776
CTF CORRECTION	RELION	4.01
MODEL FITTING	UCSF ChimeraX	1.7.dev2023
INITIAL EULER ASSIGNMENT	RELION	4.01
FINAL EULER ASSIGNMENT	RELION	4.01
CLASSIFICATION	RELION	4.01
RECONSTRUCTION	RELION	4.01
MODEL REFINEMENT	Coot	0.9.8.1
MODEL REFINEMENT	PHENIX	1.20.1

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		2436143	Particles were selected using crYOLO with a generalized picking model, followed by retraining with cleaned particle sets and repicking with a such derived optimized picking model.