6VWS

Hexamer of Helical HIV capsid by RASTR method

ELECTRON MICROSCOPY

Sample
Hexamer of helical HIV capsid protein

Specimen Preparation
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 o ...	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
Axial Symmetry	C1
Axial Rise	7.61
Angular Rotation	150.32

Map-Model Fitting and Refinement
Id	1 (6VKV)
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/Å**2)	47.36

Imaging Experiment	1
Date of Experiment
Temperature (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

EM Software
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		146291	A total of 208,225helical segments were extracted from manually selected, well-ordered helical tubes using Relion

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.