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Cryo-EM structure of human Fibroblast Activation Protein alpha in complex with H4 VNAR
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s)
Type
Source
Accession Code
Details
experimental model
Other
Sample
Fibroblast activation protein alpha in complex with H4 VNAR
Sample Components
Shark-derived variable new antigen receptor H4
Human IgG-1 Fc region of shark-derived VNAR-Fc
Human fibroblast activation protein alpha
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
332300
Reported Resolution (Å)
3.01
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Point Symmetry
C2
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
AB INITIO MODEL
Refinement Target
Overall B Value
Fitting Procedure
Details
Ab initial ModelAngelo-generated atomic model was docked into the cryo-EM density and iteratively rebuilt in Coot. Automated real-space refinement was ...
Ab initial ModelAngelo-generated atomic model was docked into the cryo-EM density and iteratively rebuilt in Coot. Automated real-space refinement was performed in Phenix using stereochemical and noncrystallographic symmetry restraints.
Data Acquisition
Detector Type
GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)
80
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
TFS KRIOS
Minimum Defocus (nm)
500
Maximum Defocus (nm)
2000
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
105000
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
EM Software
Task
Software Package
Version
PARTICLE SELECTION
cisTEM
IMAGE ACQUISITION
SerialEM
CTF CORRECTION
cisTEM
MODEL FITTING
ModelAngelo
MODEL FITTING
UCSF ChimeraX
INITIAL EULER ASSIGNMENT
cisTEM
FINAL EULER ASSIGNMENT
cisTEM
CLASSIFICATION
cisTEM
RECONSTRUCTION
cisTEM
MODEL REFINEMENT
PHENIX
MODEL REFINEMENT
Coot
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
CTF parameters were estimated in cisTEM and subsequently refined using per-particle defocus and beam-tilt refinement. CTF correction was applied during Fourier-space reconstruction.
623609
Find Particles; manual curation and 2D classification