quasi-atomic resolution model of bacteriophage PRD1 wild type virion, obtained by combined cryo-EM and X-ray crystallography.
ELECTRON MICROSCOPY
Sample
BACTERIOPHAGE PRD1
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
HOMEMADE PLUNGER
Cryogen Name
ETHANE
Sample Vitrification Details
PLUNGE VITRIFICATION
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
1800
Reported Resolution (Å)
25
Resolution Method
Other Details
THE ORIENTATIONS WERE REFINED BY THE CROSS COMMON LINES LINES METHOD (SIMPLEX) AND THE POLAR FOURIER TRANSFORM METHOD. MODEL-BASED, POLAR-FOURIER-TRAN ...
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.
Refinement Type
Symmetry Type
POINT
Point Symmetry
I
Map-Model Fitting and Refinement
Id
1 (1HX6)
Refinement Space
RECIPROCAL
Refinement Protocol
RIGID BODY FIT
Refinement Target
R-factor
Overall B Value
Fitting Procedure
Details
METHOD--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 MANU ...
METHOD--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%) REFINEMENT PROTOCOL--RIGID
BODY REFINEMENT
Data Acquisition
Detector Type
KODAK SO-163 FILM
Electron Dose (electrons/Å**2)
10
Imaging Experiment
1
Date of Experiment
1998-06-15
Temperature (Kelvin)
95
Microscope Model
FEI/PHILIPS CM200FEG
Minimum Defocus (nm)
1300
Maximum Defocus (nm)
4100
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
2
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
36000
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
200
Imaging Details
SAMPLES WERE MAINTAINED AT LIQUID NITROGEN TEMPERATURES IN THE MICROSCOPE WITH A GATAN 626-0300 CRYOTRANSFER HOLDER
