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 8VQC | pdb_00008vqc

Structure of the voltage-gated sodium channel NavPas from American Cockroach Periplaneta Americana in complex with scorpion alpha-toxin LqhaIT


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5X0M 
Sample
NavPas-LqhaIT
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsSample was applied on the grid in Vitrobot Mark IV chamber (Thermo Fisher Scientific), blotted for 4 secs with a blot force of 25 and then plunged int ...Sample was applied on the grid in Vitrobot Mark IV chamber (Thermo Fisher Scientific), blotted for 4 secs with a blot force of 25 and then plunged into ethane
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles164000
Reported Resolution (Å)3.9
Resolution MethodFSC 0.143 CUT-OFF
Other Detailsusing Cryosparc
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1 (5x0m)
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Targetmaximum likelihood
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeFEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å**2)50
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)500
Maximum Defocus (nm)1500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION4.0
CTF CORRECTIONGctf1.06
MODEL FITTINGCoot0.9.8.1
MODEL REFINEMENTPHENIX1.20
INITIAL EULER ASSIGNMENTcryoSPARC
FINAL EULER ASSIGNMENTcryoSPARC4.0.1
RECONSTRUCTIONcryoSPARC4.0.1
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION