7OOC

Mycoplasma pneumoniae 30S subunit of ribosomes in chloramphenicol-treated cells


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3J9W 
experimental modelPDB 5MMJ 
experimental modelPDB 4YBB 
Sample
cryo-electron tomograms of chloramphenicol-treated Mycoplasma pneumoniae cells
Specimen Preparation
Sample Aggregation StateCELL
Vitrification InstrumentHOMEMADE PLUNGER
Cryogen NameETHANE-PROPANE
Sample Vitrification Detailsback-side blotting for 2-3 second before plunging manual plunger without an environmental chamber
3D Reconstruction
Reconstruction MethodSUBTOMOGRAM AVERAGING
Number of Particles17890
Reported Resolution (Å)3.7
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsMap generated by focused refinement on the 30S subunit in M
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (3J9W, 5MMJ, 4YBB)
Refinement SpaceREAL
Refinement ProtocolAB INITIO MODEL
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)3.2
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1500
Maximum Defocus (nm)3750
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification81000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
MODEL REFINEMENTCoot0.9
MODEL REFINEMENTPHENIX1.18
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION