6ON2
Lon Protease from Yersinia pestis with Y2853 substrate
ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 6.144 |
f_angle_d | 0.92 |
f_chiral_restr | 0.059 |
f_plane_restr | 0.008 |
f_bond_d | 0.007 |
Sample |
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Lon protease bound to Y2853 substrate |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | HOMEMADE PLUNGER |
Cryogen Name | ETHANE |
Sample Vitrification Details | 4 uL of sample was applied per grid and manually blotted for 4 seconds followed by immediately plunge-freezing in liquid ethane cooled by liquid nitro ... |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 118143 |
Reported Resolution (Å) | 3 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | Focused classification of final reconstruction was performed on E and F "step" subunits, resulting in a reconstruction with an overall resolution of 3 ... |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C1 |
Map-Model Fitting and Refinement | |||||
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Id | 1 | ||||
Refinement Space | REAL | ||||
Refinement Protocol | AB INITIO MODEL | ||||
Refinement Target | Correlation coefficient | ||||
Overall B Value | 52 | ||||
Fitting Procedure | |||||
Details | Initial homology model was built using SWISS-MODEL and initial rigid body docking was done using UCSF Chimera |
Data Acquisition | |||||||||
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Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 52 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TALOS ARCTICA |
Minimum Defocus (nm) | 800 |
Maximum Defocus (nm) | 1200 |
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 | 36000 |
Calibrated Magnification | 43478 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 200 |
Imaging Details | Coma-free alignment procedure from Herzik & Wu, Nature Methods (2017). Preliminary grid screening was performed manually prior to data collection. |
EM Software | ||
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Task | Software Package | Version |
PARTICLE SELECTION | FindEM | 1 |
IMAGE ACQUISITION | Leginon | 3.0 |
CTF CORRECTION | RELION | 2.0b |
MODEL FITTING | Coot | 0.8.8 |
INITIAL EULER ASSIGNMENT | RELION | 2.0b |
FINAL EULER ASSIGNMENT | RELION | 2.0b |
CLASSIFICATION | RELION | 2.0b |
RECONSTRUCTION | RELION | 2.0b |
MODEL REFINEMENT | PHENIX | 1.11.1 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING ONLY | CTF correction in RELION | 1176206 | template-based cross correlation with FindEM |