4USN | pdb_00004usn

The structure of the immature HIV-1 capsid in intact virus particles at sub-nm resolution

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1L6N
experimental model	PDB	3DS2

Sample
INTACT HIV-1 PARTICLES TREATED WITH THE PROTEASE INHIBITOR AMPRENAVIR

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK II
Cryogen Name	ETHANE
Sample Vitrification Details	VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, INSTRUMENT- FEI VITROBOT MARK III, METHOD- DEGASSED C-FLAT 2- 2-2C GRIDS WERE GLOW DISCHARGED FOR 3 ...	VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, INSTRUMENT- FEI VITROBOT MARK III, METHOD- DEGASSED C-FLAT 2- 2-2C GRIDS WERE GLOW DISCHARGED FOR 30 SECONDS AT 20 MA. VIRUS SOLUTION WAS DILUTED IN PBS CONTAINING 10NM COLLOIDAL GOLD. 2 UL OF THIS MIXTURE WAS APPLIED TO A GRID. BLOTTING TIME 2 SECONDS,

3D Reconstruction
Reconstruction Method	TOMOGRAPHY
Number of Particles
Reported Resolution (Å)	8.8
Resolution Method
Other Details	SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD -2706. (DEPOSITION ID: 12684).
Refinement Type
Symmetry Type	POINT
Point Symmetry	C6

Map-Model Fitting and Refinement
Id	1 (1L6N, 3DS2)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	METHOD--FLEXIBLE REFINEMENT PROTOCOL--X-RAY,NMR

Data Acquisition
Detector Type	GATAN MULTISCAN
Electron Dose (electrons/Å**2)	40

Imaging Experiment	1
Date of Experiment	2013-08-13
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1200
Maximum Defocus (nm)	4000
Minimum Tilt Angle (degrees)	-45
Maximum Tilt Angle (degrees)	60
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	42000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	MDFF
MODEL FITTING	UCSF Chimera
RECONSTRUCTION	AV3
RECONSTRUCTION	TOM Toolbox

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	PHASE FLIPPING OF INDIVIDUAL TILTS

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 R01GM157729.