Skip to main content

 7SGF | pdb_00007sgf

Lassa virus glycoprotein construct (Josiah GPC-I53-50A) in complex with LAVA01 antibody


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5VK2 
Sample
Lassa virus glycoprotein construct(Josiah GPC-I53-50A) in complex with LAVA01 antibody (as Fab fragment)
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsBlot time 5s, Wait time 10s, Blot force 0
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles8480
Reported Resolution (Å)4.41
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsC3 symmetry was used for refinement. Solvent mask around the complex was used for refinement.
Refinement Type
Symmetry TypePOINT
Point SymmetryC3
Map-Model Fitting and Refinement
Id1 (5VK2)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)50.3
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)600
Maximum Defocus (nm)1600
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification29000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC2
IMAGE ACQUISITIONLeginon
CTF CORRECTIONGctf
MODEL FITTINGUCSF Chimera
MODEL REFINEMENTRosettaEM
MODEL REFINEMENTCoot
INITIAL EULER ASSIGNMENTRELION3.0
FINAL EULER ASSIGNMENTRELION3.0
CLASSIFICATIONRELION3.0
RECONSTRUCTIONRELION3.0
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION416326template picker