1KVP

STRUCTURAL ANALYSIS OF THE SPIROPLASMA VIRUS, SPV4, IMPLICATIONS FOR EVOLUTIONARY VARIATION TO OBTAIN HOST DIVERSITY AMONG THE MICROVIRIDAE, ELECTRON MICROSCOPY, ALPHA CARBONS ONLY


ELECTRON MICROSCOPY Experimental Data



EM Sample
Sample Vitrification Details --
Sample Aggregation State PARTICLE
Sample Reconstruction Method SINGLE PARTICLE
Name of Sample SPIROPLASMA VIRUS
EM Data Acquisition
Date of Experiment --
Temperature (Kelvin) --
Microscope Model FEI/PHILIPS EM420
Detector Type KODAK SO-163 FILM
Minimum Defocus (nm) --
Maximum Defocus (nm) 800.0
Minimum Tilt Angle (degrees) --
Maximum Tilt Angle (degrees) --
Nominal CS --
Imaging Mode BRIGHT FIELD
Electron Dose (electrons per Å**-2) 18.0
Illumination Mode FLOOD BEAM
Nominal Magnification 49000
Calibrated Magnification --
Source --
Acceleration Voltage (kV) --
Imaging Details --
3D Reconstruction
Software Package(s) --
Reconstruction Method(s) --
EM Image Reconstruction Statistics
Number of Particles --
Other Details CA TRACING OF A MODEL OF THE CAPSID PROTEIN VP1 OF SPV4 BASED ON THE CRYSTAL STRUCTURAL COORDINATES OF THE MAJOR CAPSID PROTEIN F OF PHIX174 (RESIDUES 1001 - 1427). A 71 AMINO ACID PORTION OF VP1 WAS MODELLED (GLY 226 - THR 297) AS AN INSERTION LOOP BETWEEN RESIDUES THR 1187 AND THR 1188 OF THE F CAPSID PROTEIN OF PHIX174. 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. RESIDUES 1001 - 1187 AND 1187 - 1426 ARE THE CA COORDINATES OF THE F CAPSID PROTEIN OF PHIX174. INSERTED BETWEEN RESIDUES 1187 AND 1188 IS A MODELLED CA TRACING OF A 71 AMINO ACID INSERTION LOOP OF SPV4 (RESIDUES 226 - 297) OF THE VP1 CAPSID PROTEIN, BASED ON THE CRYO-EM RECONSTRUCTION ENVELOPE AND STRUCTURAL ALIGNMENT AND SECONDARY STRUCTURE PREDICTION. THE RESOLUTION OF THE FINAL RECONSTRUCTED DENSITY MAP WAS DETERMINED TO BE AT LEAST 27 ANGSTROMS AS MEASURED BY STRUCTURE FACTOR COMPARISONS (BAKER ET AL. 1991, BIOPHYS. J. 60,1445-1456) AND FOURIER RING CORRELATION MEASUREMENTS (CONWAY ET AL. 1996, J. STRUC. BIOL. 116, 200-208)
Effective Resolution 27.0
EM Map-Model Fitting and Refinement
Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Fitting Software
RECIPROCAL -- -- -- -- --