Skip to main content

 9FDY | pdb_00009fdy

Betaglycan Orphan Domain (ratBGo) in complex with TGF-b1 and extracellular domain of TGFBRII


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 
Sample
Ternary complex of Rat Betaglycan Orphan Domain (ratBGo) with TGF-B1 and extracellular domains of TGFBRII
Sample Components
Transforming growth factor beta-1
Transforming growth factor beta receptor type-3, Orphan domain
Transforming growth factor beta receptor type-2, extracellular domain
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles235089
Reported Resolution (Å)3.4
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Target
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 ModelFEI TITAN KRIOS
Minimum Defocus (nm)1500
Maximum Defocus (nm)3500
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 SELECTIONcrYOLO1.7
PARTICLE SELECTIONTopaz
IMAGE ACQUISITIONEPU
CTF CORRECTIONGctf
MODEL FITTINGUCSF ChimeraX
MODEL REFINEMENTPHENIX
INITIAL EULER ASSIGNMENTcryoSPARCv4
FINAL EULER ASSIGNMENTcryoSPARCv4
CLASSIFICATIONRELION4.0
RECONSTRUCTIONcryoSPARC4
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION4000000