ELECTRON MICROSCOPY

Sample

Cryo-EM structure of the ternary Netrin 1-Neogenin 1-Repulsive Guidance Molecule B complex

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details Lacey carbon grids with 3 nm ultrathin carbon support film were glow discharged for 30 seconds at high RF level using Harrick Plasma Cleaner, model PDC-002-CE, and then 3.5 microl of the sample was pipetted per grid. Excess protein was blotted away for 3 seconds using filter paper (round filter paper for Vitrobot from Agar Scientific, catalogue number 47000-100) and Vitrobot Mark IV (Thermo Fisher Scientific) (relative force -15) at 95-100% humidity. Grids were plunge frozen in liquid ethane.
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 68541
Reported Resolution (Å) 5.98
Resolution Method FSC 0.143 CUT-OFF
Other Details In total 1635 movies were collected and drift correction, beam-induced motion and dose-weighting were performed with MotionCor2 RELION 3.1 (Zivanov et al., 2018) for 1635 movies. Contrast transfer function (CTF) was estimated using CTFFIND 4.1 (Rohou and Grigorieff, 2015) implemented in RELION. 280158 particles were picked using Warp (Tegunov and Cramer, 2019). 2D classification in cryoSPARC v2 (Punjani et al., 2017) were performed for these particles and best 2D class averaged with 100674 particles were used to generate ab-initio 3D model with C3 symmetry. C1 symmetry did not generate reasonable 3D model. All Warp picked particles were used for 3D classification in cryoSPARC v2 and the best class with 177056 particles was used for refinement in RELION 3.1 with initial model generated in cryoSPARC v2. Byesian particle polishing improved the resolution to 5.44 angstrom, however the map for RGMB was very weak. Last step of 3D classification without alignment with T regularisation parameter set to 16 was performed and gave one class with more continuous map for RGMB, which was refined to 5.98 angstrom resolution, as estimated using the Fourier shell correlation (FSC) = 0.143 criterion.
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space ?
Refinement Protocol RIGID BODY FIT
Refinement Target Correlation coefficient
Overall B Value ?
Fitting Procedure ?
Details Crystal structure used as a model for fitting and rigid body refinement will be described by Robinson, Griffiths, van de Haar, Malinauskas et al., Cell, 2021.
Data Acquisition
Detector Type FEI FALCON III (4k x 4k)
Electron Dose (electrons/Å2) 40
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TITAN KRIOS
Minimum Defocus (nm) -500
Maximum Defocus (nm) -700
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS ?
Imaging Mode BRIGHT FIELD
Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification 96000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
IMAGE ACQUISITION EPU ?
CTF CORRECTION CTFFIND 4.1
MODEL FITTING UCSF Chimera 1.13.1.
INITIAL EULER ASSIGNMENT RELION 3
FINAL EULER ASSIGNMENT RELION 3
CLASSIFICATION RELION 3
RECONSTRUCTION RELION 3
MODEL REFINEMENT PHENIX 1.18.2.
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?