5UYN | pdb_00005uyn

70S ribosome bound with near-cognate ternary complex not base-paired to A site codon (Structure I-nc)

ELECTRON MICROSCOPY

Sample
70S ribosome bound with near-cognate ternary complex not base-paired to A site codon (Structure I-nc)

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	GATAN CRYOPLUNGE 3
Cryogen Name	ETHANE
Sample Vitrification Details	2 uL of complex was applied to each grid. After a 10-second incubation, the grids were blotted for 2 to 4 seconds.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	4629
Reported Resolution (Å)	4
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	correlation coefficient
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	1

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	500
Maximum Defocus (nm)	5000
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	60976
Calibrated Magnification	60976
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
IMAGE ACQUISITION	SerialEM	3
CTF CORRECTION	CTFFIND	3
MODEL FITTING	UCSF Chimera	1.7
INITIAL EULER ASSIGNMENT	FREALIGN	9.11
FINAL EULER ASSIGNMENT	FREALIGN	9.11
CLASSIFICATION	FREALIGN	9.11
RECONSTRUCTION	FREALIGN	9.11
MODEL REFINEMENT	RSRef	1.1
MODEL REFINEMENT	CNS	1.3
MODEL REFINEMENT	PHENIX	1.11

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	CTFFIND3 was used to determine CTF values. FREALIGN applied CTF correction.	572417	Particles were picked from micrographs using Signature reference based particle picker.