9AXE
Cryo-EM reconstruction of a Staphylococcus aureus oleate hydratase (OhyA) assembly of dimers bound to a liposome
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 8UR3 |
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_lrange_it | 15.643 |
r_lrange_other | 15.643 |
r_dihedral_angle_6_deg | 15.284 |
r_dihedral_angle_3_deg | 13.184 |
r_scangle_it | 8.065 |
r_scangle_other | 8.065 |
r_mcangle_it | 7.051 |
r_mcangle_other | 7.051 |
r_dihedral_angle_1_deg | 4.484 |
r_scbond_it | 4.431 |
Sample |
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Assembly of dimers of OhyA bound to a liposome |
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 | 87806 |
Reported Resolution (Å) | 3.1 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Map-Model Fitting and Refinement | |||||
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Id | 1 (8UR3) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | FLEXIBLE FIT | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
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Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 50 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TALOS ARCTICA |
Minimum Defocus (nm) | 500 |
Maximum Defocus (nm) | 2500 |
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 | 79000 |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 200 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
PARTICLE SELECTION | cryoSPARC | 4 |
MODEL FITTING | Coot | |
INITIAL EULER ASSIGNMENT | cryoSPARC | 4 |
FINAL EULER ASSIGNMENT | cryoSPARC | 4 |
CLASSIFICATION | cryoSPARC | 4 |
RECONSTRUCTION | cryoSPARC | 4 |
MODEL REFINEMENT | REFMAC |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION |