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 9GOA | pdb_00009goa

Pore state of alpha-Latrotoxin


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 
Sample
tetrameric complex of alpha-latrotoxin
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK II
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles70971
Reported Resolution (Å)3.2
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsThe resolution of 3.2 Angstroem is that from focussed refinements on the core of the complex, which is the best-resolved from the maps that were used ...The resolution of 3.2 Angstroem is that from focussed refinements on the core of the complex, which is the best-resolved from the maps that were used to create the here-deposited hybrid map.
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolAB INITIO MODEL
Refinement Targetcross correlation 0.61
Overall B Value89.73
Fitting Procedure
DetailsAn Alphafold2 prediction was initially fit into the reconstruction using ChimeraX and then manually refined using Coot and energy minimized using Phen ...An Alphafold2 prediction was initially fit into the reconstruction using ChimeraX and then manually refined using Coot and energy minimized using Phenix.
Data Acquisition
Detector TypeTFS FALCON 4i (4k x 4k)
Electron Dose (electrons/Å**2)50
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)300
Maximum Defocus (nm)1700
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification215000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcrYOLO1.8.3
IMAGE ACQUISITIONEPU3.2.0.4776
CTF CORRECTIONRELION4.01
MODEL FITTINGUCSF ChimeraX1.7.dev2023
INITIAL EULER ASSIGNMENTRELION4.01
FINAL EULER ASSIGNMENTRELION4.01
CLASSIFICATIONRELION4.01
RECONSTRUCTIONRELION4.01
MODEL REFINEMENTCoot0.9.8.1
MODEL REFINEMENTPHENIX1.20.1
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION2436143Particles 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.