|Entry||Database: PDB / ID: 3iy3|
|Title||Variable domains of the computer generated model (WAM) of Fab 8 fitted into the cryoEM reconstruction of the virus-Fab 8 complex|
|Descriptor||antibody fragment from neutralizing antibody 8|
|Keywords||IMMUNE SYSTEM / cryoEM / neutralizing antibody / parvovirus / canine / feline / fab footprint|
|Specimen source||Mus musculus / mammal / ハツカネズミ, はつかねずみ /|
|Method||Electron microscopy (11.1 Å resolution / Particle / Single particle)|
|Authors||Hafenstein, S. / Bowman, V.D. / Sun, T. / Nelson, C.D. / Palermo, L.M. / Chipman, P.R. / Battisti, A.J. / Parrish, C.R. / Rossmann, M.G.|
|Citation||J. Virol., 2009, 83, 5556-5566|
SummaryFull reportAbout validation report
|Date||Deposition: Apr 9, 2009 / Release: May 12, 2009|
Downloads & links
A: antibody fragment from neutralizing antibody 8 (light chain)
B: antibody fragment from neutralizing antibody 8 (heavy chain)
Mass: 12347.646 Da / Num. of mol.: 1 / Fragment: FAb 8
Source: (natural) Mus musculus / mammal / ハツカネズミ, はつかねずみ /
Mass: 13033.718 Da / Num. of mol.: 1
Source: (natural) Mus musculus / mammal / ハツカネズミ, はつかねずみ /
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE|
|Details of virus||Empty: NO / Enveloped: NO / Virus host category: VERTEBRATES / Virus isolate: STRAIN / Virus type: VIRION|
|Natural host||Organism: Felis catus|
|Virus shell||Triangulation number (T number): 1|
|Buffer solution||Details: 10 mM Tris / pH: 7.5|
|Specimen||Conc.: 1 mg/ml / Details: 10 mM Tris / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temp: 120 K / Method: blot before plunging|
-Electron microscopy imaging
|Microscopy||Microscope model: FEI/PHILIPS CM300FEG/T / Date: Jan 23, 2004|
|Electron gun||Electron source: TUNGSTEN HAIRPIN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELD / Nominal magnification: 45000 / Calibrated magnification: 47190 / Nominal defocus max: 3.1 nm / Nominal defocus min: 1.8 nm|
Astigmatism: lens astigmatism was corrected at 100,000 times magnification
Camera length: 0 mm
|Specimen holder||Specimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: side mounted nitrogen cooled / Temperature: 93 kelvins / Temperature (max): 83 kelvins / Temperature (min): 83 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.|
|Image recording||Electron dose: 25.44 e/Å2 / Film or detector model: KODAK SO-163 FILM|
|Image scans||Sampling size: 7 microns / Details: scanned at 7 microns and bin averaged to 14 / Number digital images: 49 / Od range: 0.9 / Scanner model: ZEISS SCAI|
|Radiation||Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M|
|Radiation wavelength||Relative weight: 1|
|CTF correction||Details: robem|
|Symmetry||Point symmetry: I|
|3D reconstruction||Method: common lines / Resolution: 11.1 Å / Resolution method: FSC 0.5 CUT-OFF / Number of particles: 4344 / Symmetry type: POINT|
|Number of atoms included #LAST||Protein: 1788 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 1788|
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