MicroED structure of papain complexed with natural product E-64-A65 from microcrystals soaked in crude biosynthetic reaction mixture
ELECTRON CRYSTALLOGRAPHY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 9PAP | |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 42.2 | α = 90 |
| b = 48.78 | β = 90 |
| c = 100.1 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 21 |
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B | |||||
| ELECTRON CRYSTALLOGRAPHY | MOLECULAR REPLACEMENT | FREE R-VALUE | 2.5 | 50.05 | 1.34 | 6554 | 656 | 86.45 | 0.1847 | 0.1797 | 0.2138 | 0.2277 | 0.2593 | ||||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 8.249 |
| f_angle_d | 1.119 |
| f_chiral_restr | 0.074 |
| f_plane_restr | 0.009 |
| f_bond_d | 0.007 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| PHENIX | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| PHASER | phasing |
| Sample |
|---|
| Papain-E64-A65 complex |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | 3D ARRAY |
| Vitrification Instrument | |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | CRYSTALLOGRAPHY |
| Number of Particles | |
| Reported Resolution (Å) | 2.5 |
| Resolution Method | DIFFRACTION PATTERN/LAYERLINES |
| Other Details | |
| Refinement Type | |
| Symmetry Type | 3D CRYSTAL |
| Space Group Name | |
| Length a | 42.2 |
| Length b | 48.78 |
| Length c | 48.78 |
| Angle Alpha | 90 |
| Angle Beta | 90 |
| Angle Gamma | 90 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (9PAP) | ||||
| Refinement Space | |||||
| Refinement Protocol | |||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | DIRECT ELECTRON APOLLO (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 0.045 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS TALOS F200C |
| Minimum Defocus (nm) | 10000 |
| Maximum Defocus (nm) | 10000 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | DIFFRACTION |
| Specimen Holder Model | |
| Nominal Magnification | |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 200 |
| Imaging Details |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| NONE | ||||
