9I3O | pdb_00009i3o

Csu pilus rod type 2 stack

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7ZL4

Sample
Csu pilus rod type 2 stack

Specimen Preparation
Sample Aggregation State	2D ARRAY
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	687088
Reported Resolution (Å)	4.7
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Local Refinement allowed generating a single map without individual particles flipping and settling into pseudosymmetric orientations.
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (7ZL4)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value	330.69
Fitting Procedure
Details	UCSF Chimera was used to first fit the subunits into the single native pilus rod map (PDB Accession ID: 9I37) and average their relative angles, and i ...	UCSF Chimera was used to first fit the subunits into the single native pilus rod map (PDB Accession ID: 9I37) and average their relative angles, and it was also used to adjust pixel spacing of all maps to match model dimensions. Coot was used to adjust side chain and loop positions. A pair of antiparallel pili with subunit angles adjusted to 3-turns-per-7-subunits symmetry was overlapped with a 2D class to adjust the binding junction angle. Finally, Phenix was used to fit the type 2 stack model into the map.

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	59.848

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	400
Maximum Defocus (nm)	1600
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	105000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	v4.5.3
IMAGE ACQUISITION	EPU	v3.60
CTF CORRECTION	cryoSPARC	v4.5.3
MODEL FITTING	UCSF Chimera	1.15
MODEL FITTING	Coot	0.8.9.2 EL
MODEL REFINEMENT	PHENIX	1.20.1_4487:
INITIAL EULER ASSIGNMENT	cryoSPARC	v4.5.3
FINAL EULER ASSIGNMENT	cryoSPARC	v4.5.3
CLASSIFICATION	cryoSPARC	v4.5.3
RECONSTRUCTION	cryoSPARC	v4.5.3

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		30605819	Two different types of Csu pilus stack architectures were solved from the same particle set. Particle picking failed to distinguish between the two, so the initial number of particles is the same for both stack architectures.