5A20

Structure of bacteriophage SPP1 head-to-tail interface filled with DNA and tape measure protein


ELECTRON MICROSCOPY
Sample
BACTERIOPHAGE SPP1 HEAD- TO-TAIL INTERFACE
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK II
Cryogen NameETHANE
Sample Vitrification DetailsVITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- FEI VITROBOT
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles14000
Reported Resolution (Å)7.6
Resolution Method
Other DetailsATOMIC 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-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 TypePOINT
Point SymmetryC6
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
DetailsMETHOD--FLEXIBLE REFINEMENT PROTOCOL--X-RAY, NMR, PREDICTION
Data Acquisition
Detector TypeKODAK SO-163 FILM
Electron Dose (electrons/Å**2)20
Imaging Experiment1
Date of Experiment2008-10-09
Temperature (Kelvin)
Microscope ModelFEI TECNAI F30
Minimum Defocus (nm)900
Maximum Defocus (nm)3600
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification39000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
MODEL FITTINGFlex-EM
MODEL FITTINGMODELLER
MODEL FITTINGUCSF Chimera
MODEL FITTINGVEDA
RECONSTRUCTIONEMAN
RECONSTRUCTIONIMAGIC
RECONSTRUCTIONSPIDER
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
EACH PARTICLE