ELECTRON MICROSCOPY

Sample

Hexamer of helical HIV capsid protein

Specimen Preperation
Sample Aggregation State HELICAL ARRAY
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details ?
3D Reconstruction
Reconstruction Method HELICAL
Number of Particles 245050
Reported Resolution (Å) 6.08
Resolution Method FSC 0.143 CUT-OFF
Other Details A non-helical approach (RASTR) to calculate a volume from the same subset of data used for helical analysis. The position and rotation to the center of a single hexamer in the final helical volume was determined and used along the final refined helical rise and twist to extract a total of 245050 unique particles from which surrounding tube density was subtracted by reprojection using Relion. The resulting stack of 245050 particles, each extracted into a 192 multiple 192 pixel box centered around the chosen asymmetric unit for each subtracted volume, was imported into Cryosparc. 2D clustering and ab-initio heterogeneous reconstruction with 4 volumes were then used to select a subset of 96392 particle images. These images, along with the cleanest reference from ab-initio volume determination were then used to obtain a volume through 3D Refinement.
Refinement Type
Symmetry Type HELICAL
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol RIGID BODY FIT
Refinement Target ?
Overall B Value 204.64
Fitting Procedure ?
Details ?
Data Acquisition
Detector Type GATAN K3 (6k x 4k)
Electron Dose (electrons/Å2) 47.36
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TALOS ARCTICA
Minimum Defocus (nm) 1200
Maximum Defocus (nm) 2500
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 28000
Calibrated Magnification 28000
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 200
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION RELION 3.0.4
IMAGE ACQUISITION Leginon ?
CTF CORRECTION CTFFIND 4.0
MODEL FITTING UCSF Chimera ?
INITIAL EULER ASSIGNMENT RELION 3.0.4
FINAL EULER ASSIGNMENT RELION 3.0.4
CLASSIFICATION cryoSPARC 2.0
RECONSTRUCTION cryoSPARC 2.0
MODEL REFINEMENT PHENIX 3758
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
NONE ?