ELECTRON MICROSCOPY Experimental Data



EM Sample
Sample Vitrification Details PLUNGE VITRIFICATION SAMPLES PREPARED AS THIN LAYERS OF VITREOUS ICE MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626-0300 CRYOTRANSFER HOLDER.
Sample Aggregation State PARTICLE
Sample Reconstruction Method SINGLE PARTICLE
Name of Sample SEMLIKI FOREST VIRUS
EM Data Acquisition
Date of Experiment 1998-06-15
Temperature (Kelvin) 95.0
Microscope Model FEI/PHILIPS CM200FEG
Detector Type KODAK SO-163 FILM
Minimum Defocus (nm) 975.0
Maximum Defocus (nm) 7600.0
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) 10.0
Illumination Mode OTHER
Nominal Magnification 50000
Calibrated Magnification --
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 200
Imaging Details --
3D Reconstruction
Software Package(s) PYPFT
Reconstruction Method(s) SIMPLEX Procedure
EM Image Reconstruction Statistics
Number of Particles 5267
Other Details THE ORIENTATIONS WERE REFINED BY THE CROSS COMMON LINES LINES METHOD (SIMPLEX) AND THE POLAR FOURIER TRANSFORM METHOD USING A PARALLEL IMPLEMENTATION (PYPFT). THE EFFECTIVE RESOLUTION OF THE FINAL RECONSTRUCTED DENSITY WAS DETERMINED TO BE AT LEAST 9 ANGSTROMS, AS MEASURED BY RANDOMLY SPLITTING THE PARTICLES INTO TWO SETS AND CALCULATING THE FOURIER SHELL CORRELATION OBTAINED FROM SEPARATE RECONSTRUCTIONS (HARAUZ AND VAN HEEL 1986, OPTIK 73, 146-156). THE EIGENVALUE SPECTRUM GAVE AN INDICATION OF THE RANDOMNESS OF THE DATA THAT WAS INCLUDED IN THE RECONSTRUCTION. THE COMPLETENESS OF THE DATA WAS VERIFIED IN THAT ALL EIGENVALUES EXCEEDED 100. THE COORDINATES ARE IN THE P, Q, R FRAME IN ANGSTROM UNITS AND CORRESPOND TO ICOSAHEDRAL SYMMETRY AXES. THE ORIGIN IS CHOSEN AT THE CENTER OF THE VIRUS WITH P, Q AND R ALONG MUTUALLY PERPENDICULAR TWO-FOLD AXES OF THE ICOSAHEDRON. THEY SHOULD REMAIN IN THAT FRAME FOR THE EASE OF THE USER IN CREATING THE BIOLOGICALLY SIGNIFICANT VIRAL COMPLEX PARTICLE USING THE 60 ICOSAHEDRAL SYMMETRY OPERATORS. RESIDUES NOT VISIBLE IN THE ORIGINAL CRYSTAL STRUCTURES ARE NOT INCLUDED IN THE CRYO-EM STRUCTURE MODEL. FOR EXAMPLE, C RESIDUES 1-118, ARE NOT VISIBLE IN THE CRYSTAL STRUCTURE (PDB ENTRY 1VCQ) AND THEREFORE ARE NOT INCLUDED IN THE COORDINATES BELOW.
Effective Resolution 9.0
EM Map-Model Fitting and Refinement
Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Fitting Software
REAL RIGID BODY FIT R-factor -- -- --