8I8R | pdb_00008i8r

Cryo-EM Structure of OmpC3-MlaA Complex in MSP2N2 Nanodiscs

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5NUP

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.352
f_angle_d	1.146
f_chiral_restr	0.066
f_bond_d	0.006
f_plane_restr	0.006

Sample
Outer membrane complex of OmpC-MlaA with periplasmic MlaC reconstituted in MSP2N2 nanodiscs
Sample Components
Outer membrane porin C
Intermembrane phospholipid transport system lipoprotein MlaA

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	205487
Reported Resolution (Å)	2.93
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (5NUP, 5NUP, 5NUP, 5NUP)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	Cross-correlation coefficient
Overall B Value	88
Fitting Procedure
Details	Building of the high-resolution structures of OmpC-MlaA was done via approximate fitting using the OmpC-MlaA crystal structure (PDB 5NUP) as rigid bodies into the density in Chimera, followed by refinement in COOT.

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	90

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	800
Maximum Defocus (nm)	2000
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	105000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	4.0.0
IMAGE ACQUISITION	SerialEM
CTF CORRECTION	cryoSPARC	4.0.0
MODEL FITTING	UCSF Chimera	1.15
MODEL FITTING	Coot	0.9.4.1 EL
INITIAL EULER ASSIGNMENT	cryoSPARC	4.0.0
FINAL EULER ASSIGNMENT	cryoSPARC	4.0.0
CLASSIFICATION	cryoSPARC	4.0.0
RECONSTRUCTION	cryoSPARC	4.0.0
MODEL REFINEMENT	PHENIX	1.20.1-4487

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	Patch CTF routine in cryoSPARC	2434319	We performed automated particle picking using Blob and Template Picker for initial template picking and final sampling respectively.