5A21 | pdb_00005a21

Structure of bacteriophage SPP1 head-to-tail interface without DNA and tape measure protein

ELECTRON MICROSCOPY

Sample
BACTERIOPHAGE SPP1 HEAD- TO-TAIL INTERFACE

Specimen Preparation
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	18000
Reported Resolution (Å)	7.2
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. ...	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-2994. (DEPOSITION ID: 13332).
Refinement Type
Symmetry Type	POINT
Point Symmetry	C6

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/Å**2)	20

Imaging Experiment	1
Date of Experiment	2008-10-09
Temperature (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
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	39000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
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

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.