9YGM | pdb_00009ygm

ELECTRON MICROSCOPY

Sample
80S ribosome

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

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

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.