ELECTRON MICROSCOPY

Sample

BACTERIOPHAGE SPP1 HEAD- TO-TAIL INTERFACE

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK II
Cryogen Name ETHANE
Sample Vitrification Details VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- FEI VITROBOT
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 14000
Reported Resolution (Å) 7.6
Resolution Method ?
Other Details ATOMIC COORDINATES FOR GP6, GP15, GP16, GP17 WERE OBTAINED FROM PDB FILES 2JES (LEBEDEV ET AL., EMBO J., 2007, 26, 1984), 2KBZ, 2KCA (LHUILLIER ET AL., PROC.NATL.ACAD.SCI. USA, 2009, 106, 8507), 2LFP (CHAGOT ET AL., PROTEINS, 2012, 80, 319), CORRESPONDIGLY, AND DOCKED INTO EM ELECTRON DENSITY MAP USING FLEXIBLE FIT. ATOMIC COORDINATES FOR MISSING DOMAINS OF GP6 AND GP17.1. WERE MODELLED USING I-TASSER PROTEIN STRUCTURE PREDICTION SERVER (Y ZHANG, BMC BIOINFORMATICS, 2008, 9, 40) AND DOCKED INTO EM ELECTRON DENSITY MAP USING FLEXIBLE FIT. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2993. (DEPOSITION ID: 13331). SEQUENCE N-TERMINAL RESIDUES 1-28 AND C-TERMINAL RESIDUES 468-509 WERE NOT INCLUDED IN THE ATOMIC COORDINATES USED FOR DOCKING DUE TO DIFFICULTIES TRACING CORRESPONDING DENSITIES IN THE EM MAP. ASN 365 IS SUBSTITUTED FOR LYS, SAME AS IN PDB COORDINATE FILE 2JES, WHICH WAS USED AS A STARTING POINT FOR THE FITTING. N-TERMINAL RESIDUES 1-3 ARE OMITTED FROM THE DOCKED GP15 SEQUENCE. PRO 6 IS SUBSTITUTED WITH ARG IN GP16 SEQUENCE, AS IT IS IN THE PDB COORDINATE FILE 2KCA USED FOR FITTING N-TERMINAL RESIDUE 1 IS MISSING FROM THE DOCKED GP17 SEQUENCE. N-TERMINAL RESIDUES 1-8 AND C-TERMINAL RESIDUES 170-177 ARE MISSING FROM THE DOCKED GP17.1 SEQUENCE DUE TO DIFFICULTIES TRACING CORRESPONDING DENSITIES IN THE EM MAP.
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol FLEXIBLE FIT
Refinement Target ?
Overall B Value ?
Fitting Procedure ?
Details METHOD--FLEXIBLE REFINEMENT PROTOCOL--X-RAY, NMR, PREDICTION
Data Acquisition
Detector Type KODAK SO-163 FILM
Electron Dose (electrons/Å2) 20
Imaging Experiment
Date of Experiment 2008-10-09
Temprature (Kelvin)
Microscope Model FEI TECNAI F30
Minimum Defocus (nm) 900
Maximum Defocus (nm) 3600
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS 2.0
Imaging Mode BRIGHT FIELD
Specimen Holder Model .
Nominal Magnification 39000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
MODEL FITTING Flex-EM ?
MODEL FITTING MODELLER ?
MODEL FITTING UCSF Chimera ?
MODEL FITTING VEDA ?
RECONSTRUCTION EMAN ?
RECONSTRUCTION IMAGIC ?
RECONSTRUCTION SPIDER ?
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
? EACH PARTICLE