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 11YB | pdb_000011yb

Structure of AlphaIIbBeta3-R21C11 Fab in the near-bent conformation


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3FSC 
experimental modelPDB 7LA4 
Sample
The structure of AlphaIIbBeta3-R21C11 Fab in the near-bent conformation
Sample Components
Integrin AlphaIIbbeta3
R21C11 Fab
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK I
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles49648
Reported Resolution (Å)3.4
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1 (8T2V, 8T2V, 7LA4, 7LA4)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)54
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)1500
Maximum Defocus (nm)2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification81000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARCv4.4.0
CTF CORRECTIONcryoSPARCv4.4.0
MODEL FITTINGUCSF Chimeraversion 1.16
INITIAL EULER ASSIGNMENTcryoSPARCv4.4.0
FINAL EULER ASSIGNMENTcryoSPARCv4.4.0
CLASSIFICATIONcryoSPARCv4.4.0
RECONSTRUCTIONcryoSPARCv4.4.0
MODEL REFINEMENTPHENIXversion 1.20.1-4487
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION1332000