3DNY | pdb_00003dny

Fitting of the eEF2 crystal structure into the cryo-EM density map of the eEF2.80S.AlF4-.GDP complex

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1N0U

Sample
eEF2-bound 80S complex in presence of AlF4-, and GDP

Specimen Preparation
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
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (1N0U)
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	1
Date of Experiment
Temperature (Kelvin)	93
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

EM Software
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