Experiment: 6YE4

Structure of ExbB pentamer from Serratia marcescens by single particle cryo electron microscopy

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5SV0

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	23.0627
f_angle_d	1.5558
f_chiral_restr	0.1023
f_bond_d	0.0262
f_plane_restr	0.01

Sample
Homopentamer of ExbB

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	LEICA EM CPC
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	157111
Reported Resolution (Å)	3.2
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C5

Map-Model Fitting and Refinement
Id	1 (5SV0)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	Correlation coefficient
Overall B Value	55.3
Fitting Procedure
Details	the ExbB sequence from S. marcescens was modeled by homology from the 5SV0 monomer from E. coli using Phyre software and the pentamer was generated us ...	the ExbB sequence from S. marcescens was modeled by homology from the 5SV0 monomer from E. coli using Phyre software and the pentamer was generated using the 5SV0 symmetry. real space refinement was carried out with rigid body, simulated annealing and morphing steps.

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	55.95

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1500
Maximum Defocus (nm)	2500
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	165000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	RELION	3.0
IMAGE ACQUISITION	SerialEM
CTF CORRECTION	Gctf	1.06
CTF CORRECTION	RELION	3.0
MODEL FITTING	UCSF Chimera	1.15
MODEL REFINEMENT	PHENIX	1.14
INITIAL EULER ASSIGNMENT	RELION	3.0
FINAL EULER ASSIGNMENT	RELION	3.0
CLASSIFICATION	RELION	3.0
RECONSTRUCTION	RELION	3.0

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
NONE		1291382