ELECTRON MICROSCOPY Experimental Data



EM Sample
Sample pH 7.2
Sample Support Details HOLEY CARBON
Sample Vitrification Details PLUNGE VITRIFICATION
Sample Aggregation State PARTICLE
Name of Sample BACTERIOPHAGE PRD1
Sample Details 400 MESH COPPER GLOW DISCHARGE SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE
EM Data Acquisition
Date of Experiment 1998-06-15
Num of Micrographs-Images Used 12
Temperature (Kelvin) 95.0
Microscope Model PHILIPS CM200 FEG
Detector Type KODAK SO-163 FILM
Minimum Defocus (nm) 1300.0
Maximum Defocus (nm) 4100.0
Minimum Tilt Angle (degrees) 0.0
Maximum Tilt Angle (degrees) 0.0
Nominal CS 2.0
Imaging Mode LOW DOSE
Electron Dose (electrons nm**-2) 1000.0
Illumination Mode BRIGHT FIELD
Nominal Magnification 36000
Calibrated Magnification --
Source FEG
Acceleration Voltage (kV) 200
Imaging Details SAMPLES WERE MAINTAINED AT LIQUID NITROGEN TEMPERATURES IN THE MICROSCOPE WITH A GATAN 626-0300 CRYOTRANSFER HOLDER
3D Reconstruction
Software Package(s)
Reconstruction Method ICOSAHEDRAL
EM Image Reconstruction Statistics
Number of Particles 861
Nominal Pixel Size 3.68
Actual Pixel Size 3.42
Effective Resolution 25.0
EM Reconstruction Magnification Callibration THE PIXEL SIZE OF THE CRYO-EM MAP WAS OBTAINED USING THE X-RAY STRUCTURE OF THE P3 TRIMER AS A REFERENCE. AFTER AN INITIAL FITTING USING THE NOMINAL PIXEL SIZE, THE P3 TRIMERS IN THE ICOSAHEDRAL ASYMMETRIC UNIT WERE GRADUALLY TRANSLATED TOWARDS THE CENTER OF THE PARTICLE UNTIL THE CRYSTALLOGRAPHIC R-FACTOR WAS MINIMISED.
Other Details THE ORIENTATIONS WERE REFINED BY THE CROSS COMMON LINES LINES METHOD (SIMPLEX) AND THE POLAR FOURIER TRANSFORM METHOD. MODEL-BASED, POLAR-FOURIER-TRANSFORM (FULLER ET AL. 1996, J.STRUC.BIOL. 116, 48-55; BAKER AND CHENG, 1996, J.STRUC.BIOL. 116, 120-130) MODEL-BASED CROSS COMMON LINES SEARCH AND REFINEMENT (CROWTHER ET AL. 1970, NATURE (LONDON) 226, 421-425; FULLER ET AL. 1996, J.STRUC.BIOL. 116, 48-55; FERLENGHI ET AL. 1998, J.MOL.BIOL. 283, 71-81). THE EFFECTIVE RESOLUTION OF THE FINAL RECONSTRUCTED DENSITY WAS DETERMINED TO BE AT LEAST 25 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.
EM Map-Model Fitting and Refinement
Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Fitting Software
RECIPROCAL RIGID BODY REFINEMENT R-FACTOR -- THE CRYSTAL STRUCTURE OF THE MAJOR COAT PROTEIN P3 (PDB FILE 1HX6) WAS PLACED INTO THE CRYO-EM DENSITY MAP. THE CAPSID PROTEIN WAS FIRST MANUALLY POSITIONED INTO THE CRYO-EM DENSITY CORRESPONDING TO POSITIONS OF THE FOUR INDEPENDENT TRIMERS IN THE ICOSAHEDRAL ASYMMETRIC UNIT. THESE POSITIONS WERE THEN REFINED BY RIGID BODY REFINEMENT IN RECIPROCAL SPACE WITH THE PROGRAM XPLOR. QUALITY OF THE FIT R- FACTOR= 0.360, CROSS-CORRELATI0N COEFFICIENT 0.880, ATOMS OUTSIDE DENSITY PER ICOSAHEDRAL ASYMMETRIC UNIT 801 (2.3%), ATOM CLASHES PER ICOSAHEDRAL ASYMMETRIC UNIT 69 (0.2%) --