ELECTRON MICROSCOPY

Sample

Henipavirus nipahense

Specimen Preperation
Sample Aggregation State 3D ARRAY
Vitrification Instrument LEICA EM GP
Cryogen Name ETHANE
Sample Vitrification Details ?
3D Reconstruction
Reconstruction Method SUBTOMOGRAM AVERAGING
Number of Particles 9767
Reported Resolution (Å) 7
Resolution Method FSC 0.143 CUT-OFF
Other Details ?
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol RIGID BODY FIT
Refinement Target CC
Overall B Value 351
Fitting Procedure ?
Details The initial model of 1 M Dimer was generated with AlphaFold2. Model was docked into map in Chimera v1.1.4. RealSpaceRefine in Phenix of 1 M Dimer. Open refined model and map in Chimera. Duplicate model, rotate and dock. Re run RealSpaceRefine. Repeat for all dimers present in electron density map. Run comprehensive validation in Phenix which resulted in Ramachandran outliers of 0%, Allowed 7% and Favored of 93% . We then removed all side chains from model prior to PDB deposition since our map does not support any side chain density - only backbone.
Data Acquisition
Detector Type GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å2) 3.65
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TALOS ARCTICA
Minimum Defocus (nm) 1500
Maximum Defocus (nm) 3500
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS 2.7
Imaging Mode BRIGHT FIELD
Specimen Holder Model ?
Nominal Magnification 63000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 200
Imaging Details ?
Imaging Experiment
Task Software Package Version
VOLUME SELECTION Dynamo 1.1.532
IMAGE ACQUISITION SerialEM 4.0.1
CTF CORRECTION CTFFIND 4
MODEL FITTING UCSF Chimera 1.1.4
MODEL REFINEMENT PHENIX 1.21_5207
FINAL EULER ASSIGNMENT RELION 4.0 Tomo
RECONSTRUCTION RELION 4.0 Tomo
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?
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