ELECTRON MICROSCOPY Experimental Data



Virus Particulars
Virus Host Category Virus Host Species Virus Host Growth Cell Virus Type Virus Isolate ICTVDB ID
BACTERIA(EUBACTERIA) Escherichia coli E. coli slyD BACTERIA(EUBACTERIA) SPECIES 00.042.0.81.007
EM Sample
Sample Concentration (mg/ml) 8.0
Sample pH 7.5
Sample Aggregation State PARTICLE
Name of Sample Procapsid of the bacteriophage alpha3
EM Data Acquisition
Date of Experiment 1998-10-16
Num of Micrographs-Images Used --
Temperature (Kelvin) 88.0
Microscope Model FEI/PHILIPS CM200FEG/ST
Detector Type KODAK SO163 FILM
Minimum Defocus (nm) 3200.0
Maximum Defocus (nm) 1600.0
Minimum Tilt Angle (degrees) 0.0
Maximum Tilt Angle (degrees) 0.0
Nominal CS 2.0
Imaging Mode BRIGHT FIELD
Electron Dose (electrons nm**-2) 0.017
Illumination Mode --
Nominal Magnification 38000
Calibrated Magnification 40000
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 200
Imaging Details --
3D Reconstruction
Software Package(s)
Reconstruction Method Model based polar fourier transform (Projection matching).
EM Image Reconstruction Statistics
Number of Particles 2378
Nominal Pixel Size 1.84
Actual Pixel Size 1.75
Effective Resolution 16.0
CTF Correction Method CTF correction was done for each particle.
EM Reconstruction Magnification Callibration Magnification correction was determined using the F pentamer as found in the mature virion of alpha3 and phix174 and in the closed procapsid as a control. Symmetry related contacts in the control were found to be 6.3% of all atoms. The pixel size of the reconstruction was adjusted so as to obtain the same number of contacts.
Other Details 2378 particles were included in the final reconstruction. The effective resolution is 15.0-16.0A. Higher resolution was not possible because of the tendency of particles to orient themselves non-randomly. Only CA coordinates are presented in the entry.
EM Map-Model Fitting and Refinement
Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Fitting Software
REAL rigid molecule fit using the program EMfit Best fit criterion used by the program EMfit is based on the average value of the density at all atomic sites in the fitted protein, the lack of atoms in negative density, and the absence of symmetry related atomic clashes. -- General search followed by a climb procedure EMfit