Experiment: 6RWY

Export apparatus core and inner rod of the Shigella type 3 secretion system

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6F2D
experimental model	PDB	2MME

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	11.61
f_angle_d	0.805
f_chiral_restr	0.043
f_plane_restr	0.006
f_bond_d	0.004

Sample
Export apparatus core, inner rod and start of the needle of the Shigella type 3 secretion system
Sample Components
Export apparatus core
Inner rod
Needle

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	Sample applied on grid 5 ul, incubation time 5 min on ice, then moved into Vitrobot and 5 ul sample applied again. Blot time: 2 sec Blot force: -2 Dra ...	Sample applied on grid 5 ul, incubation time 5 min on ice, then moved into Vitrobot and 5 ul sample applied again. Blot time: 2 sec Blot force: -2 Drain time: 0 sec

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	72298
Reported Resolution (Å)	5.11
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (6F2D, 6F2D, 6F2D, 2MME)
Refinement Space	REAL
Refinement Protocol
Refinement Target	Cross-correlation coefficient
Overall B Value	162
Fitting Procedure
Details

Data Acquisition
Detector Type	FEI FALCON II (4k x 4k)
Electron Dose (electrons/Å**2)	25

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1.5
Maximum Defocus (nm)	4
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	101179
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	RELION	1.4
CTF CORRECTION	CTFFIND	3.5
MODEL FITTING	UCSF Chimera	1.13.1
MODEL FITTING	iMODFIT	1.44
INITIAL EULER ASSIGNMENT	RELION	2.1
FINAL EULER ASSIGNMENT	RELION	2.1
CLASSIFICATION	RELION	2.1
RECONSTRUCTION	RELION	2.1
MODEL REFINEMENT	PHENIX	3409

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		171833