7UAF
Human meprin alpha inhibitory complex with compound 10d (N~3~,N~3~-bis[(2H-1,3-benzodioxol-5-yl)methyl]-N-hydroxy-beta-alaninamide)
ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 22.455 |
f_angle_d | 1.801 |
f_chiral_restr | 0.104 |
f_plane_restr | 0.02 |
f_bond_d | 0.012 |
Sample |
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Tetrameric portion of helical meprin alpha in complex with a small molecule inhibitor |
Specimen Preparation | |
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Sample Aggregation State | FILAMENT |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details | 3 s blot, -3 force |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 235162 |
Reported Resolution (Å) | 2.4 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C1 |
Map-Model Fitting and Refinement | |||||
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Id | 1 (4GWN) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | FLEXIBLE FIT | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
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Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 44.5 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 500 |
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 | 130000 |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
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Task | Software Package | Version |
PARTICLE SELECTION | crYOLO | 1.8.1 |
IMAGE ACQUISITION | EPU | |
CTF CORRECTION | CTFFIND | 4.1.13 |
CTF CORRECTION | Warp | 1.0.7 |
MODEL FITTING | ISOLDE | 1.1.0 |
MODEL FITTING | UCSF ChimeraX | 1.3 |
MODEL FITTING | Coot | 0.9.2 |
MODEL REFINEMENT | ISOLDE | 1.1.0 |
MODEL REFINEMENT | PHENIX | 1.17 |
INITIAL EULER ASSIGNMENT | RELION | 2.1, 3.1 |
FINAL EULER ASSIGNMENT | cryoSPARC | 3.3.1 |
FINAL EULER ASSIGNMENT | RELION | 3.1 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 925458 | Subparticles extracted after particle expansion about pseudo-helical symmetry |