Dye Type Peroxidase Aa from Streptomyces lividans by microcrystal electron diffraction (MicroED/3D ED)
ELECTRON CRYSTALLOGRAPHY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 6I43 | |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 72.77 | α = 90 |
| b = 67.4 | β = 105.8 |
| c = 73.63 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 1 |
Data Collection
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) | R-Free Selection Details | Mean Isotropic B | ||||
| ELECTRON CRYSTALLOGRAPHY | MOLECULAR REPLACEMENT | FREE R-VALUE | 2.4 | 19.46 | 1.34 | 46115 | 2962 | 87.76 | 0.2053 | 0.2019 | 0.2242 | 0.2561 | 0.2735 | Random selection | 18.52 | ||||
| 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 | 9.3745 |
| f_angle_d | 0.5571 |
| f_chiral_restr | 0.0388 |
| f_plane_restr | 0.0049 |
| f_bond_d | 0.0025 |
| Sample |
|---|
| Dye type peroxidase Aa |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | 3D ARRAY |
| Vitrification Instrument | |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Manual blotting in room temperature with ambient humidity |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | CRYSTALLOGRAPHY |
| Number of Particles | |
| Reported Resolution (Å) | 2.4 |
| Resolution Method | DIFFRACTION PATTERN/LAYERLINES |
| Other Details | |
| Refinement Type | |
| Symmetry Type | 3D CRYSTAL |
| Space Group Name | |
| Length a | 72.77 |
| Length b | 67.4 |
| Length c | 67.4 |
| Angle Alpha | 90 |
| Angle Beta | 105.8 |
| Angle Gamma | 90 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (6I43) | ||||
| Refinement Space | RECIPROCAL | ||||
| Refinement Protocol | OTHER | ||||
| Refinement Target | Maximum-likelihood | ||||
| Overall B Value | 18.52 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI CETA (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 0.115 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | |
| Maximum Defocus (nm) | |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | DIFFRACTION |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| MODEL FITTING | PHENIX | |
| MOLECULAR REPLACEMENT | PHENIX | |
| CRYSTALLOGRAPHY MERGING | PHENIX | |
| RECONSTRUCTION | PHENIX | |
| MODEL REFINEMENT | PHENIX | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| NONE | ||||
