7B9K
Cryo-EM structure of the dihydrolipoyl transacetylase cubic core of the E. coli pyruvate dehydrogenase complex including lipoyl domains
ELECTRON MICROSCOPY
Sample |
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dihydrolipoyl transacetylase cubic core of the pyruvate dehydrogenase complex |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details | 3 microliters of sample, blot force 0, 15 second wait time, 3 second blot time |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details | 3 microliters of sample, blot force 0, 15 second wait time, 3 second blot time |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details | 2.5 microliters of sample, blot force 0, 15 second wait time, 3 second blot time |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 29434 |
Reported Resolution (Å) | 3.16 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | O |
Map-Model Fitting and Refinement | |||||
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Id | 1 (4N72, 1QJO) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | RIGID BODY FIT | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
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Detector Type | GATAN K2 QUANTUM (4k x 4k) | GATAN K2 QUANTUM (4k x 4k) | GATAN K2 QUANTUM (4k x 4k) | ||||||
Electron Dose (electrons/Å**2) | 30 | 28.11 | 28.11 |
Imaging Experiment | 1 | 2 | 3 |
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Date of Experiment | |||
Temperature (Kelvin) | |||
Microscope Model | FEI TITAN KRIOS | FEI TITAN KRIOS | FEI TITAN KRIOS |
Minimum Defocus (nm) | |||
Maximum Defocus (nm) | |||
Minimum Tilt Angle (degrees) | |||
Maximum Tilt Angle (degrees) | |||
Nominal CS | 2.7 | 2.7 | 2.7 |
Imaging Mode | BRIGHT FIELD | BRIGHT FIELD | BRIGHT FIELD |
Specimen Holder Model | |||
Nominal Magnification | |||
Calibrated Magnification | |||
Source | FIELD EMISSION GUN | FIELD EMISSION GUN | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 | 300 | 300 |
Imaging Details |
EM Software | ||
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Task | Software Package | Version |
PARTICLE SELECTION | cryoSPARC | 2.15 |
IMAGE ACQUISITION | EPU | |
CTF CORRECTION | cryoSPARC | 2.15 |
MODEL FITTING | PHENIX | 1.16 |
INITIAL EULER ASSIGNMENT | cryoSPARC | 2.15 |
FINAL EULER ASSIGNMENT | cryoSPARC | 2.15 |
CLASSIFICATION | cryoSPARC | 2.15 |
RECONSTRUCTION | cryoSPARC | 2.15 |
MODEL REFINEMENT | PHENIX | 1.16 |
MODEL REFINEMENT | REFMAC | 5.8.0232 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 799790 | automated template picking in CryoSPARC |