1HB5

quasi-atomic resolution model of bacteriophage PRD1 P3-shell, obtained by combined cryo-EM and X-ray crystallography.

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HX6

Sample
BACTERIOPHAGE PRD1 P3 SHELL

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	471
Reported Resolution (Å)	12
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= 0.312, CROSS-CORRELATION COEFFICIENT 0.933, ATOMS OUTSIDE DENSITY PER ICOSAHEDRAL ASYMMETRIC UNIT 180 (0.7%), ATOM CLASHES PER ICOSAHEDRAL ASYMMETRIC UNIT 121 (0.5%) 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 ELECTRON MICROSCOPE WITH A GATAN 626-0300 CRYOTRANSFER HOLDER.

EM Software
Task	Software Package	Version
MODEL FITTING	EMfit
MODEL FITTING	O
MODEL FITTING	X-PLOR

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.