9OQA | pdb_00009oqa

Cryo-EM structure of AaaA, a Pseudomonas Aeruginosa autotransporter

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.202
f_angle_d	0.484
f_chiral_restr	0.037
f_bond_d	0.003
f_plane_restr	0.003

Sample
AaaA complex with Arginine

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	During vitrification 3 ul of sample placed on a grid and then vitrified with 10s hold and 4s blot time.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	241938
Reported Resolution (Å)	3.87
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Final map reconstructed from local refinement following non-uniform refinement to improve the region of interest excluding the detergent belt in cryoSPARC. Mask of the region of interest used to do the local refinement.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

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

Data Acquisition
Detector Type	FEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å**2)	44.71

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TALOS ARCTICA
Minimum Defocus (nm)	400
Maximum Defocus (nm)	1600
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	130000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	4.4.1
PARTICLE SELECTION	Topaz	2.4
IMAGE ACQUISITION	EPU	3.8
CTF CORRECTION	cryoSPARC	4.4.1
MODEL FITTING	UCSF Chimera	1.17.3
INITIAL EULER ASSIGNMENT	cryoSPARC	4.4.1
FINAL EULER ASSIGNMENT	cryoSPARC	4.4.1
CLASSIFICATION	RELION	4.0.1
RECONSTRUCTION	cryoSPARC	4.4.1
MODEL REFINEMENT	PHENIX	1.21.2-5419
MODEL REFINEMENT	Coot	0.9.8.96

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	Patch CTF in CryoSPARC	3009424	Particles picked using topaz train following blob and template picking in cryoSPARC.