ELECTRON CRYSTALLOGRAPHY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 9DHO | |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 67.64 | α = 90 |
| b = 67.64 | β = 90 |
| c = 106.67 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 43 21 2 |
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-Free (Depositor) | Mean Isotropic B | |||||||
| ELECTRON CRYSTALLOGRAPHY | FREE R-VALUE | 1.3 | 43.64 | 1.33 | 58442 | 2868 | 95.01 | 0.1908 | 0.1888 | 0.2279 | 12.61 | ||||||||
| 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 | 12.9065 |
| f_angle_d | 1.0181 |
| f_chiral_restr | 0.0848 |
| f_bond_d | 0.0091 |
| f_plane_restr | 0.0085 |
| Sample |
|---|
| Proteinase K |
| 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) | 1.3 |
| Resolution Method | DIFFRACTION PATTERN/LAYERLINES |
| Other Details | |
| Refinement Type | |
| Symmetry Type | 3D CRYSTAL |
| Space Group Name | |
| Length a | 67.64 |
| Length b | 67.64 |
| Length c | 67.64 |
| Angle Alpha | 90 |
| Angle Beta | 90 |
| Angle Gamma | 90 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (9dho) | ||||
| Refinement Space | RECIPROCAL | ||||
| Refinement Protocol | OTHER | ||||
| Refinement Target | Maximum likelihood | ||||
| Overall B Value | 12.61 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON IV (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 0.002 | ||||||||
| 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 | 4.2.0 |
| MODEL FITTING | Coot | 0.9.8.93 |
| MODEL REFINEMENT | PHENIX | 1.21.1 |
| MOLECULAR REPLACEMENT | PHASER | 2.8.3 |
| SYMMETRY DETERMINATION | XDS | BUILT=20230630 |
| CRYSTALLOGRAPHY MERGING | XSCALE | BUILT=20230630 |
| RECONSTRUCTION | PHENIX | 1.21.1 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| NONE | ||||
