6PWB | pdb_00006pwb

Rigid body fitting of flagellin FlaB, and flagellar coiling proteins, FcpA and FcpB, into a 10 Angstrom structure of the asymmetric flagellar filament purified from Leptospira biflexa Patoc WT cells resolved via subtomogram averaging


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5WJT 
experimental modelPDB 6NQW 
experimental modelPDB 6NQZ 
Sample
Flagellar filament purified from the periplasm of the Spirochete bacterium, Leptospira biflexa
Specimen Preparation
Sample Aggregation StateFILAMENT
Vitrification InstrumentFEI VITROBOT MARK III
Cryogen NameETHANE
Sample Vitrification Details2 minute incubation time; blot time of 6-7.5 seconds; and blot offset of -2 mm
3D Reconstruction
Reconstruction MethodSUBTOMOGRAM AVERAGING
Number of Particles10581
Reported Resolution (Å)9.83
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsemClarity: The two half-dataset volumes were combined with a B-170 factor of 0, and the Gold standard FSC at 0.143 was calculated to be 9.83 A with an ...emClarity: The two half-dataset volumes were combined with a B-170 factor of 0, and the Gold standard FSC at 0.143 was calculated to be 9.83 A with anisotropic resolutions ranging from 8.89-16.17 Angstrom.
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (5WJT, 6NQW, 6NQZ)
Refinement SpaceRECIPROCAL
Refinement ProtocolRIGID BODY FIT
Refinement TargetCorrelation coefficient
Overall B Value
Fitting Procedure
DetailsEliminate minor clashes between FlaB1, FcpA, and FcpB
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)1.7
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI POLARA 300
Minimum Defocus (nm)3000
Maximum Defocus (nm)5000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2
Imaging ModeBRIGHT FIELD
Specimen Holder ModelSIDE ENTRY, EUCENTRIC
Nominal Magnification15000
Calibrated Magnification19230
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
VOLUME SELECTIONPEET1.11
VOLUME SELECTIONRELION2.1
IMAGE ACQUISITIONSerialEM3
CTF CORRECTIONIMOD4.9.4_RHEL6-64_CUDA8.0
CTF CORRECTIONRELION2.1.b1-gcccuda-2016.10-cc37
CTF CORRECTIONemClarity1..0
MODEL FITTINGRosetta3
MODEL FITTINGSitus2.8-foss-2016b
MODEL FITTINGUCSF Chimera1.12
FINAL EULER ASSIGNMENTRELION2.1.b1-gcccuda-2016.10-cc37
FINAL EULER ASSIGNMENTemClarity1.0
RECONSTRUCTIONemClarity1.1
MODEL REFINEMENTRosetta3
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTIONCTF estimation was initially done in IMOD.