7NWT | pdb_00007nwt

Initiated 70S ribosome in complex with 2A protein from encephalomyocarditis virus (EMCV)

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5MDZ

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.055
f_angle_d	0.8065
f_chiral_restr	0.048
f_bond_d	0.0103
f_plane_restr	0.0059

Sample
Initiated 70S ribosome in complex with 2A protein from encephalomyocarditis virus (EMCV)

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	Quantifoil R 2/2 400-mesh copper supports were coated with an additional ~ 60 angstrom layer of amorphous, evaporated carbon by flotation and thorough ...	Quantifoil R 2/2 400-mesh copper supports were coated with an additional ~ 60 angstrom layer of amorphous, evaporated carbon by flotation and thoroughly dried before use. Grids were made hydrophilic by glow-discharge in air for 30 s. Three microliters of crosslinking reaction was applied to grids which were then blotted for 4.5 s and vitrified by plunging into liquid ethane using a Vitrobot MK IV (FEI) at 277K, 100% relative humidity.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	120749
Reported Resolution (Å)	2.66
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (5MDZ)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	Correlation coefficient
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	FEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)	54.4

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1200
Maximum Defocus (nm)	3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	75000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	RELION	3.1
IMAGE ACQUISITION	EPU	2.0
CTF CORRECTION	CTFFIND	4
CTF CORRECTION	RELION	3.1
MODEL FITTING	UCSF Chimera	1.15
INITIAL EULER ASSIGNMENT	RELION	3.1
FINAL EULER ASSIGNMENT	RELION	3.1
CLASSIFICATION	RELION	3.1
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	PHENIX	1.91.1-4122
MODEL REFINEMENT	PHENIX	1.91.1-4122

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	The contrast transfer function (CTF) was estimated per-image using CtfFind4. All further phase+amplitude correction was performed internally in Relion. Per-particle CTF refinement was done after polishing	820475	Reference-free autopicking of particles was performed using the Laplacian-of-Gaussian function in Relion (200 - 250 angstrom diameter)