6XZC | pdb_00006xzc

CryoEM structure of the ring-shaped virulence factor EspB from Mycobacterium tuberculosis

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4XXX

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.497
f_angle_d	0.585
f_chiral_restr	0.038
f_plane_restr	0.007
f_bond_d	0.004

Sample
EspB Heptameric complex

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	0.05% fluorinated octylmaltoside was add into protein solution and immediately applied to a freshly glow-discharged holey carbon grid. ). Excess liquid was blotted for 2.3 s using an FEI Vitrobot Mark IV and the sample was plunge frozen in liquid ethane.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	143350
Reported Resolution (Å)	3.37
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C7

Map-Model Fitting and Refinement
Id	1 (4XXX)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	30

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1500
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
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	CTFFIND	4
MODEL FITTING	Coot
MODEL REFINEMENT	PHENIX	1.17
INITIAL EULER ASSIGNMENT	cryoSPARC	2.0
FINAL EULER ASSIGNMENT	cryoSPARC
CLASSIFICATION	cryoSPARC
RECONSTRUCTION	cryoSPARC	2.0

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		292964