5TCP

Near-atomic resolution cryo-EM structure of the periplasmic domains of PrgH and PrgK


ELECTRON MICROSCOPY
Sample
Type III secretion injectisome basal body
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles67800
Reported Resolution (Å)4.3
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsLimited frequency refinement in Frealign
Refinement Type
Symmetry TypePOINT
Point SymmetryC24
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
DetailsInitial fitting was carried out with Chimera, followed by rebuilding and refinement in Rosetta, Phenix, and Coot.
Data Acquisition
Detector TypeGATAN K2 QUANTUM (4k x 4k)
Electron Dose (electrons/Å**2)1.3
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1500
Maximum Defocus (nm)3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS0.01
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification64000
Calibrated Magnification29240
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONEMAN2
PARTICLE SELECTIONRELION
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONCTFFIND
INITIAL EULER ASSIGNMENTRELION
INITIAL EULER ASSIGNMENTFREALIGN
FINAL EULER ASSIGNMENTFREALIGN
RECONSTRUCTIONFREALIGN
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION263900