8I8R
Cryo-EM Structure of OmpC3-MlaA Complex in MSP2N2 Nanodiscs
ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
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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 |
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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 | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details |
3D Reconstruction | |
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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 bod ... |
Data Acquisition | |||||||||
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Detector Type | GATAN K3 (6k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 90 |
Imaging Experiment | 1 |
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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 | ||||
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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. |