9SYH | pdb_00009syh

E. coli 70S ribosome from deltaRlmE strain

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8CGK
experimental model	PDB	8CGJ
experimental model	PDB	8CF1
experimental model	PDB	7K00
in silico model	AlphaFold

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
s_angle_nonh_d	1.46723681
s_bond_nonh_d	0.0107450424

Sample
70S 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	515288
Reported Resolution (Å)	1.89
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (8CGK, 8CGJ, 8CF1, 7K00)
Refinement Space	RECIPROCAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value	104.76
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	42.1

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	700
Maximum Defocus (nm)	1500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC
IMAGE ACQUISITION	EPU	2.12.1
CTF CORRECTION	cryoSPARC	4.4
MODEL FITTING	Coot	0.9.8.95
INITIAL EULER ASSIGNMENT	cryoSPARC
FINAL EULER ASSIGNMENT	cryoSPARC	4.4
RECONSTRUCTION	cryoSPARC	4.4
MODEL REFINEMENT	Servalcat	0.4.77

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		736925

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.