9YGM | pdb_00009ygm

Babesia divergens ribosome structure by single-particle cryo-EM (3D class3, E-site tRNA)

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold
experimental model	PDB	5XXU
experimental model	PDB	5XXB
experimental model	PDB	3J7A

Sample
80S ribosome

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	261009
Reported Resolution (Å)	2.7
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (5XXU, 5XXB, 5XXB, 5XXB, 5XXB, 3J7A)
Refinement Space
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	Initial docking and fitting was done in UCSF ChimeraX for the ribosomal proteins using AlphaFold2 predicted models, except for eL41; the T. gondii eL4 ...	Initial docking and fitting was done in UCSF ChimeraX for the ribosomal proteins using AlphaFold2 predicted models, except for eL41; the T. gondii eL41 chain (PDB 5XXB) served as the initial model. The T. gondii PDBs 5XXU and 5XXB were also fit with UCSF ChimeraX and used for initial model building of the Babesia divergens rRNAs.

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
IMAGE ACQUISITION	SerialEM
MODEL REFINEMENT	PHENIX	1.21.2_5419+SVN
RECONSTRUCTION	RELION	30001

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