REL PDBe PDBe PDBe 2006-06-29 2006-06-29 2006-09-05 2013-09-25 West Nile virus in complex with the Fab fragment of a neutralizing monoclonal antibody. Kaufmann B Nybakken GE Chipman PR Zhang W Diamond MS Fremont DH Kuhn RJ Rossmann MG Kaufmann B Nybakken GE Chipman PR Zhang W Diamond MS Fremont DH Kuhn RJ Rossmann MG West Nile virus in complex with the Fab fragment of a neutralizing monoclonal antibody. PROC.NAT.ACAD.SCI.USA 103 12400 12404 2006 16895988 doi:10.1073/pnas.0603488103 West Nile virus NY99 complexed with Fab fragment of neutralizing monoclonal antibody E16 West Nile virus NY99 complexed with Fab fragment of neutralizing monoclonal antibody E16 T1 icosahedron with three E monomers and two Fab per asymmetric unit 2 West Nile virus West Nile virus Homo sapiens VERTEBRATES E glycoprotein 500 1 VIRION STRAIN true false WNV E16 Fab fragment unidentified 120 Monomer true mammalian cell line singleParticle particle 8.0
12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA
400 mesh copper grid
 ETHANE HOMEMADE PLUNGER
Vitrification instrument: Guillotine-style plunge freezeing device
A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. Once the ethane in the vial is completely frozen, it needs to be slightly melted. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot of excess buffer, sufficient to leave a thin layer on the grid. After a predetermined time, the filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen, and the grid is transferred under liquid nitrogen to a storage box immersed liquid nitrogen for later use in the microscope. FEI/PHILIPS CM300FEG/T FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.0 1.32 3.88 47000.0 47190.0 GATAN LIQUID NITROGEN 98 live FFT at 200K mag
low dose
KODAK SO-163 FILM OTHER 6.35 78 22
Nikon SuperCoolScan 9K scanned images binned 2x2
16. EUCENTRIC 0 0
The particles were selected interactively at the computer terminal.
Each particle
 I OTHER 14.5 FSC 0.5 CUT-OFF PFTSEARCH, PO2R, P3DR
final map includes data to 12.8 Ang resolution (fsc 0.3 cut-off); magnification of final map standardized to a map calculated from dengue virus model coordinates (PDB accession no 1THD)
3567
theta 69 to 90 degrees phi -31 to 31 degrees omega 0 to 360 degrees
 emd_1234.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 301 301 301 -150 -150 -150 301 301 301 826.51587 826.51587 826.51587 90.0 90.0 90.0 X Y Z -1499.927734379999947 11314.149414060000709 703.748352049999994 1973.494140629999947 2.7459 2.7459 2.7459 611.0 AUTHOR map of West Nile Virus complexed with Fab fragment of neutralizing antibody E16
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 1THD