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 4D1K | pdb_00004d1k

Cryo-electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly.


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4COP 
Sample
HIV-1 CANC Y169 MUTANT PROTEIN ASSEMBLED WITH 73MER DNA INTO TUBULAR PARTICLES
Specimen Preparation
Sample Aggregation StateHELICAL ARRAY
Vitrification InstrumentHOMEMADE PLUNGER
Cryogen NameETHANE
Sample Vitrification DetailsVITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, INSTRUMENT- HOMEMADE PLUNGER,
3D Reconstruction
Reconstruction MethodHELICAL
Number of Particles
Reported Resolution (Å)9.4
Resolution Method
Other DetailsATOMIC MODELS WERE FITTED USING MOLECULAR MOLECULAR DYNAMICS FLEXIBLE FITTING (MDFF). THE CA-NTD ATOMIC MODEL PDB ID 2JPR AND THE CA-CTD ATOMIC MODEL ...ATOMIC MODELS WERE FITTED USING MOLECULAR MOLECULAR DYNAMICS FLEXIBLE FITTING (MDFF). THE CA-NTD ATOMIC MODEL PDB ID 2JPR AND THE CA-CTD ATOMIC MODEL PDB ID 4COP WERE USED AS STARTING MODELS. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2638. (DEPOSITION ID: 12470).
Refinement Type
Symmetry TypeHELICAL
Map-Model Fitting and Refinement
Id1 (4COP)
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
DetailsMETHOD--FLEXIBLE REFINEMENT PROTOCOL--X-RAY
Data Acquisition
Detector TypeKODAK SO-163 FILM
Electron Dose (electrons/Å**2)23
Imaging Experiment1
Date of Experiment2012-12-25
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)4500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
MODEL FITTINGMDFF
MODEL FITTINGUCSF Chimera
RECONSTRUCTIONAV3
RECONSTRUCTIONSPIDER