ELECTRON MICROSCOPY Experimental Data



Virus Particulars
Virus Host Category Virus Host Species Virus Host Growth Cell Virus Type Virus Isolate ICTVDB ID
VERTEBRATES Homo sapiens -- VIRION OTHER --
EM Sample
Sample Vitrification Details Blot for 0.7 seconds before plunging into liquid ethane (GATAN CRYOPLUNGE 3).
Sample Aggregation State PARTICLE
Sample Reconstruction Method SINGLE PARTICLE
Name of Sample Mature HPV16 quasivirus capsid complexed with H16.V5 Fabs
EM Data Acquisition
Date of Experiment 2013-10-30
Temperature (Kelvin) 95.0
Microscope Model JEOL 2100
Detector Type GATAN ULTRASCAN 4000 (4k x 4k)
Minimum Defocus (nm) 690.0
Maximum Defocus (nm) 3990.0
Minimum Tilt Angle (degrees) 0.0
Maximum Tilt Angle (degrees) 0.0
Nominal CS 2.0
Imaging Mode BRIGHT FIELD
Electron Dose (electrons per Å**-2) 15.0
Illumination Mode SPOT SCAN
Nominal Magnification 80000
Calibrated Magnification --
Source LAB6
Acceleration Voltage (kV) 200
Imaging Details --
3D Reconstruction
Software Package(s) Auto3DEM, EMAN
Reconstruction Method(s) --
EM Image Reconstruction Statistics
Number of Particles 2075
Other Details Semi-automatic particle selection was performed using e2boxer.py to obtain the particle coordinates, followed by particle boxing, linearization, normalization, and apodization of the images using Robem. Defocus and astigmatism values to perform contrast transfer function (CTF) correction were assessed using Robem for the extracted particles. The icosahedrally averaged reconstructions were initiated using a random model generated with setup_rmc and reached 14 A resolution estimated at a Fourier Shell Correlation (FSC) of 0.5. For the last step of refinement, the final maps were CTF-corrected using a B factor of 200 A2. (Single particle--Applied symmetry: I)
Effective Resolution 13.6
EM Map-Model Fitting and Refinement
Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Fitting Software
REAL FLEXIBLE FIT -- -- -- --