ELECTRON MICROSCOPY

Sample

2:1 complex of the mouse thrombopoietin receptor ectodomain and mouse thrombopoietin

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details Blot time of 4 s, blot force of 6 and no wait time or drain time.
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 745000
Reported Resolution (Å) 3.6
Resolution Method FSC 0.143 CUT-OFF
Other Details Final map was generated using Non-uniform refinement followed by 3DFlex refinement in cryoSPARC. Map was sharpened by deepEMhancer.
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol FLEXIBLE FIT
Refinement Target Cross-correlation coefficient
Overall B Value ?
Fitting Procedure ?
Details ChimeraX was used to perform rigid-body fitting of domains and modelling was performed using Coot and ISOLDE. Refinement was carried out in PHENIX.
Data Acquisition
Detector Type GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å2) 50.57
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TITAN KRIOS
Minimum Defocus (nm) 400
Maximum Defocus (nm) 3600
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 130000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION cryoSPARC 4.2.1
IMAGE ACQUISITION EPU 2
CTF CORRECTION cryoSPARC 4.2.1
MODEL FITTING ISOLDE 1.6.0
MODEL FITTING UCSF ChimeraX 1.6.1
MODEL FITTING Coot 0.9.8.3
INITIAL EULER ASSIGNMENT cryoSPARC 4.2.1
FINAL EULER ASSIGNMENT cryoSPARC 4.2.1
CLASSIFICATION cryoSPARC 4.2.1
RECONSTRUCTION cryoSPARC 4.2.1
MODEL REFINEMENT PHENIX 1.20.1_4487
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
NONE Defocus values were estimated using patch CTF estimation and CTF correction was performed during 3D reccnstruction.
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