ELECTRON CRYSTALLOGRAPHY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 7SKW | |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 26.66 | α = 87.73 |
| b = 31.15 | β = 108.97 |
| c = 33.57 | γ = 111.6 |
| Symmetry | |
|---|---|
| Space Group | P 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 | FREE R-VALUE | 0.83 | 11.73 | 1.96 | 87855 | 2000 | 98.29 | 0.1762 | 0.1755 | 0.2094 | 0.2064 | 0.2282 | Random selection | 11.04 | |||||
| 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 | 6.3402 |
| f_angle_d | 1.2195 |
| f_chiral_restr | 0.1137 |
| f_bond_d | 0.0188 |
| f_plane_restr | 0.0113 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 992 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 147 |
| Heterogen Atoms | 7 |
| Sample |
|---|
| Lysozyme |
| 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) | 0.83 |
| Resolution Method | DIFFRACTION PATTERN/LAYERLINES |
| Other Details | |
| Refinement Type | |
| Symmetry Type | 3D CRYSTAL |
| Space Group Name | |
| Length a | 26.66 |
| Length b | 31.15 |
| Length c | 31.15 |
| Angle Alpha | 111.6 |
| Angle Beta | 108.97 |
| Angle Gamma | 111.6 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (7SKW) | ||||
| Refinement Space | RECIPROCAL | ||||
| Refinement Protocol | OTHER | ||||
| Refinement Target | maximum-likelihood | ||||
| Overall B Value | 11.04 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI CETA (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 1.52 | ||||||||
| 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 |
| RECONSTRUCTION | PHENIX | |
| MODEL REFINEMENT | PHENIX | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| NONE | ||||
