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Withdrawn samples were spotted directly onto freshly glow-discharged holey carbon grids, blotted for 1-2 s, and flash frozen in liquid ethane using a ...
Withdrawn samples were spotted directly onto freshly glow-discharged holey carbon grids, blotted for 1-2 s, and flash frozen in liquid ethane using a Vitrobot Mark IV plunger (ThermoFisher Scientific) after a wait time of 40 s at 4 degrees Celsius.
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
63618
Reported Resolution (Å)
3.28
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Point Symmetry
C1
Map-Model Fitting and Refinement
Id
1 (7N1P)
Refinement Space
REAL
Refinement Protocol
OTHER
Refinement Target
CC
Overall B Value
87.2
Fitting Procedure
Details
The atomic model of the E. coli 70S ribosome was initially docked into the postprocessed density maps with UCSF Chimera and manually adjusted in Coot. ...
The atomic model of the E. coli 70S ribosome was initially docked into the postprocessed density maps with UCSF Chimera and manually adjusted in Coot. As the modelled mRNA represents a mixture of all isolated native E. coli mRNAs bound to polysomes, a random sense mRNA sequence was chosen, except for the five codons, which were adjusted to the anticodons. Ligand restraints were generated using phenix.eLBOW. The full-length model for protein bS1 was generated using AlphaFold and manually placed and adjusted in Coot. All models were refined over multiple rounds using the module phenix.real_space_refine in PHENIX and interactive model building and refinement in Coot, using libG restraints for the RNAs. The quality of all refined models was assessed using the comprehensive model validation function in PHENIX and wwPDB validation server.