6VEJ | pdb_00006vej

TriABC transporter from Pseudomonas aeruginosa

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3NE5
experimental model	PDB	3LNN
experimental model	PDB	2V4D

Sample
TriABC

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

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	35220
Reported Resolution (Å)	4.5
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (3NE5, 3LNN, 2V4D)
Refinement Space	REAL
Refinement Protocol	AB INITIO MODEL
Refinement Target
Overall B Value
Fitting Procedure
Details	Subunits A-C were modeled by I-TASSER using CusA (3NE5) and then fitted into the EM density and refined with Phenix and model rebuilt using Coot. The N-terminal regions of subunits P-R were modeled by I-TASSER based on MP domain of 3LNN while C-terminal regions of subunits P-R were modelled based on MP domain of 2V4D and similarly refined and model rebuilt.

Data Acquisition
Detector Type	FEI FALCON II (4k x 4k)
Electron Dose (electrons/Å**2)	50

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1600
Maximum Defocus (nm)	3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	75000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	EMAN2
IMAGE ACQUISITION	EPU
CTF CORRECTION	CTFFIND	4
INITIAL EULER ASSIGNMENT	RELION	1.3
FINAL EULER ASSIGNMENT	RELION	1.3
RECONSTRUCTION	RELION	1.3

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		35530