In situ 3D ED/MicroED nanovolume structure of Magnaporthe grisea Woronin Body Major protein crystallized in cellulo
ELECTRON CRYSTALLOGRAPHY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1KHI | |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 57.382 | α = 90 |
| b = 57.382 | β = 90 |
| c = 198.122 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 65 2 2 |
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B | ||||||
| ELECTRON CRYSTALLOGRAPHY | FREE R-VALUE | 2.2 | 11.685 | 9244 | 499 | 87.538 | 0.214 | 0.2111 | 0.2427 | 0.2576 | 0.2906 | 47.112 | |||||||
| 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] | |
| 0.07 | 0.035 | 0.07 | -0.227 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 22.265 |
| r_dihedral_angle_6_deg | 13.687 |
| r_dihedral_angle_3_deg | 11.666 |
| r_lrange_other | 11.101 |
| r_lrange_it | 11.098 |
| r_dihedral_angle_1_deg | 8.36 |
| r_scangle_it | 8.018 |
| r_scangle_other | 8.013 |
| r_mcangle_it | 6.241 |
| r_mcangle_other | 6.238 |
| Sample |
|---|
| Trichoplusia ni insect cell |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | 3D ARRAY |
| Vitrification Instrument | LEICA PLUNGER |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | CRYSTALLOGRAPHY |
| Number of Particles | |
| Reported Resolution (Å) | 2.2 |
| Resolution Method | DIFFRACTION PATTERN/LAYERLINES |
| Other Details | |
| Refinement Type | |
| Symmetry Type | 3D CRYSTAL |
| Space Group Name | |
| Length a | 57.38 |
| Length b | 57.38 |
| Length c | 57.38 |
| Angle Alpha | 120 |
| Angle Beta | 90 |
| Angle Gamma | 120 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (1KHI) | ||||
| Refinement Space | RECIPROCAL | ||||
| Refinement Protocol | OTHER | ||||
| Refinement Target | |||||
| Overall B Value | 51 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 0.0009 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS 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 |
| IMAGE ACQUISITION | SerialEM | |
| MODEL FITTING | Coot | |
| MODEL REFINEMENT | REFMAC | |
| CRYSTALLOGRAPHY MERGING | AIMLESS | |
| RECONSTRUCTION | Coot | |
| RECONSTRUCTION | REFMAC | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| NONE | ||||
