Home
About
Browse
Covid-19
Organism Classification
Alphafold Collection
Virus Classification
Indian Data
Contact
Search Type
PDB Id
Uniprot Id
Source Organism
Host Organism
Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
3DNY
pdb_00003dny
10.2210/pdb3dny/pdb
Download file
FASTA
PDB
MMCIF
Binary MMCIF
XML
Structure Factors
Full Validation Report
Validation File (XML)
Validation File (CIF)
FASTA Zipped(.gz)
PDB Zipped(.gz)
MMCIF Zipped(.gz)
Binary MMCIF Zipped(.gz)
Structure Factors Zipped(.gz)
Validation File Zipped (.xml.gz)
Validation File Zipped (.cif.gz)
ELECTRON MICROSCOPY
Sample
eEF2-bound 80S complex in presence of AlF4-, and GDP
Specimen Preperation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK I
Cryogen Name
ETHANE
Sample Vitrification Details
?
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
?
Reported Resolution (Å)
12.6
Resolution Method
?
Other Details
supervised classification was used (ref. Valle, M. et al, 2002, EMBO J.)
Refinement Type
Symmetry Type
POINT
Map-Model Fitting and Refinement
ID
1
Refinement Space
REAL
Refinement Protocol
RIGID BODY FIT
Refinement Target
?
Overall B Value
?
Fitting Procedure
?
Details
METHOD--Each domain fitted as rigid body, domains I (G and G), II,IV, and V were fitted. Domain III, and domain IV insertions were not included in this fitting model. The coordinates for this entry are based on manual fitting of the coordinates of the crystal structure 1N0U into cryo-EM density map. Therefore, authors did not deposit new structure factors.
Data Acquisition
Detector Type
KODAK SO-163 FILM
Electron Dose (electrons/Å
2
)
10
Imaging Experiment
Date of Experiment
?
Temprature (Kelvin)
Microscope Model
FEI TECNAI F20
Minimum Defocus (nm)
4500
Maximum Defocus (nm)
1500
Minimum Tilt Angle (degrees)
?
Maximum Tilt Angle (degrees)
?
Nominal CS
?
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
?
Nominal Magnification
50000
Calibrated Magnification
49650
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
200
Imaging Details
?
Imaging Experiment
Task
Software Package
Version
MODEL FITTING
O
?
RECONSTRUCTION
SPIDER
?
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
.
segregation in defocus groups and correction in volumes