9YXB | pdb_00009yxb

Babesia divergens ribosome structure by single-particle cryo-EM (3D class1, A-, P-, and E-site tRNAs and mRNA)

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	Other
experimental model	PDB	9YGM

Sample
80S ribosome
Sample Components
40S
60S

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	26467
Reported Resolution (Å)	3.1
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (9YGM, 9YGM, 9YGM, 9YGM)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	Protein chains were built de novo with ModelAngelo. The rRNA chains from PDB 9YGM, which corresponds to the highest-resolution conformational class (3DC3, 80S with E-site tRNA) from the same dataset, were rigid-body fit and remodeled. The complete model then underwent iterative rounds of manual adjustment in Coot and real-space refinement in Phenix.

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	42

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	800
Maximum Defocus (nm)	2200
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	105000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	crYOLO
MODEL REFINEMENT	PHENIX	1.21.2_5419+SVN
IMAGE ACQUISITION	EPU
RECONSTRUCTION	RELION	5

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		1259788