9CL9 | pdb_00009cl9

WT 12C IM fraction, B-b3 with RluB bound

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4YBB
experimental model	PDB	8RPY
in silico model	AlphaFold	AF-A0A828LEY7-F1

Sample
WT 12C 50S ribosomal subunit assembly intermediate

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	3 microliter of the sample was added.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	22502
Reported Resolution (Å)	5.04
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (4YBB, 8RPY, 8RPY, 8RPY, 8RPY, 8RPY, 8RPY, 8RPY, 8RPY, 8RPY, 8RPY)
Refinement Space	REAL
Refinement Protocol	OTHER
Refinement Target	Comprehensive validation (cryo-EM)
Overall B Value	118.8
Fitting Procedure
Details	The atomic model was fitted into a low resolution (5 angstrom) EM map; therefore the coordinates should only serve as a general visual representation ...	The atomic model was fitted into a low resolution (5 angstrom) EM map; therefore the coordinates should only serve as a general visual representation and should not be looked into detail. Initial docking of the atomic model was done in ChimeraX. Coot and Phenix were used for real-space refinements. Geometry minimization in Phenix was used to improve the RNA atomic model.

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	50

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TALOS ARCTICA
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	36000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details	In order to account for highly preferred orientation of the specimen, data were acquired using tilts at -20 degrees.

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC
IMAGE ACQUISITION	Leginon
MODEL FITTING	UCSF ChimeraX
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	Coot
MODEL REFINEMENT	PHENIX

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
NONE	CTF correction were performed by Patch CTF Estimation of cryoSPARC

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.