7UWR
KSQ+AT from first module of the pikromycin synthase
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2QO3 |
Sample |
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Pik127 |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details | Blotted for 3 seconds with a force of "1" before plunging. |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 184737 |
Reported Resolution (Å) | 2.61 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | Density modification in Phenix |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C2 |
Map-Model Fitting and Refinement | |||||
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Id | 1 (2QO3) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | FLEXIBLE FIT | ||||
Refinement Target | Phenix | ||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
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Detector Type | GATAN K3 (6k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 70 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 800 |
Maximum Defocus (nm) | 1500 |
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 | |
Calibrated Magnification | 61728 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details | Collected 4284 movies at 0 degrees tilt and 2912 movies at -30 degrees tilt |
EM Software | ||
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Task | Software Package | Version |
IMAGE ACQUISITION | SerialEM | |
CTF CORRECTION | cryoSPARC | 3.2.0 |
MODEL FITTING | UCSF ChimeraX | 1.1.1 |
MODEL FITTING | PHENIX | 1.19.2-4158 |
INITIAL EULER ASSIGNMENT | cryoSPARC | 3.2.0 |
FINAL EULER ASSIGNMENT | cryoSPARC | 3.2.0 |
CLASSIFICATION | cryoSPARC | 3.2.0 |
RECONSTRUCTION | cryoSPARC | 3.2.0 |
MODEL REFINEMENT | Coot | 0.8.9.2 |
MODEL REFINEMENT | PHENIX | 1.19.2-4158 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | CTF correction performed by cryosparc during reconstruction | 6761206 | From blob picker, 6,761,206 particles were selected. Then, from template picker, 2,350,020 particles were selected. |