9JQO | pdb_00009jqo

Polyrod formed by FlgG (G65V) from the Salmonella TH26292 strain


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7CBM 
Sample
Polyrod composed of FlgG(G65V)
Specimen Preparation
Sample Aggregation StateFILAMENT
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameNITROGEN
Sample Vitrification Detailsblotting time of 4 seconds, 1 seconds drain time, force 0
Staining TypeNEGATIVE
Staining MaterialUranyl acetate
Staining DetailsThe condition and concentration of purified samples were checked before making cryoEM sample grid. A 3 microliter aliquot of the sample solutions was ...The condition and concentration of purified samples were checked before making cryoEM sample grid. A 3 microliter aliquot of the sample solutions was placed on a thin carbon-coated, 20 seconds glow-discharged copper grid. The extra solution was removed from the grid by blotting, the filaments and cells were stained with 2% and 0.2% phosphotungstic acid (PTA), respectively, and the purified protein samples were stained with 2% uranyl acetate. The sample grids were dried for 1 hour at room temperature and checked using a transmission electron microscope, JEM-1011 (JEOL, Akishima, Japan) with an accelerating voltage of 100 kV.
3D Reconstruction
Reconstruction MethodHELICAL
Number of Particles88969
Reported Resolution (Å)3.37
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypeHELICAL
Axial SymmetryC1
Axial Rise4.31
Angular Rotation64.9
Map-Model Fitting and Refinement
Id1 (7CBM)
Refinement SpaceREAL
Refinement ProtocolOTHER
Refinement Target
Overall B Value
Fitting Procedure
DetailsPhenix1.21-rc1 , refmac servalcat and ISOLDE was used for fitting, and Phenix was used for final fitting.
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)75
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelJEOL CRYO ARM 300
Minimum Defocus (nm)200
Maximum Defocus (nm)2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification50000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC3.2.0
MODEL REFINEMENTPHENIX1.21rc1_5127
CTF CORRECTIONcryoSPARC3.2.0
CLASSIFICATIONcryoSPARC3.2.0
RECONSTRUCTIONcryoSPARC3.2.0
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION386473