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 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)
TypeSourceAccession CodeDetails
experimental modelPDB 1L6N 
experimental modelPDB 3DS2 
Sample
INTACT HIV-1 PARTICLES TREATED WITH THE PROTEASE INHIBITOR AMPRENAVIR
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK II
Cryogen NameETHANE
Sample Vitrification DetailsVITRIFICATION 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 MethodTOMOGRAPHY
Number of Particles
Reported Resolution (Å)8.8
Resolution Method
Other DetailsSUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD -2706. (DEPOSITION ID: 12684).
Refinement Type
Symmetry TypePOINT
Point SymmetryC6
Map-Model Fitting and Refinement
Id1 (1L6N, 3DS2)
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
DetailsMETHOD--FLEXIBLE REFINEMENT PROTOCOL--X-RAY,NMR
Data Acquisition
Detector TypeGATAN MULTISCAN
Electron Dose (electrons/Å**2)40
Imaging Experiment1
Date of Experiment2013-08-13
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1200
Maximum Defocus (nm)4000
Minimum Tilt Angle (degrees)-45
Maximum Tilt Angle (degrees)60
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification42000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
MODEL FITTINGMDFF
MODEL FITTINGUCSF Chimera
RECONSTRUCTIONAV3
RECONSTRUCTIONTOM Toolbox
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING OF INDIVIDUAL TILTS