6RWX | pdb_00006rwx

Periplasmic inner membrane ring of the Shigella type 3 secretion system

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GR0
experimental model	PDB	2Y9J

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.429
f_angle_d	0.881
f_chiral_restr	0.058
f_bond_d	0.009
f_plane_restr	0.006

Sample
The periplasmic inner membrane ring of the Shigella type 3 secretion system

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 Drain time: 0 sec

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	72298
Reported Resolution (Å)	3.55
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C24

Map-Model Fitting and Refinement
Id	1 (3GR0, 2Y9J)
Refinement Space	REAL
Refinement Protocol	AB INITIO MODEL
Refinement Target	Correlation coefficient and geometry
Overall B Value	140
Fitting Procedure
Details	Model was built and refined in the map low-pass filtered at 3.2 A

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	1.11.2
MODEL FITTING	Coot	0.8.8
INITIAL EULER ASSIGNMENT	RELION	2.1
FINAL EULER ASSIGNMENT	RELION	2.1
CLASSIFICATION	RELION	2.1
RECONSTRUCTION	RELION	2.1
MODEL REFINEMENT	PHENIX	1.13-2998

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