7SKW
Ab initio structure of triclinic lysozyme from electron-counted MicroED data
ELECTRON CRYSTALLOGRAPHY
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 26.42 | α = 88.319 |
| b = 30.72 | β = 109.095 |
| c = 33.01 | γ = 112.075 |
| Symmetry | |
|---|---|
| Space Group | P 1 |
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 | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
| ELECTRON CRYSTALLOGRAPHY | FREE R-VALUE | 0.87 | 19.876 | 64974 | 3168 | 87.578 | 0.198 | 0.1969 | 0.2214 | Random selection | 12.188 | ||||||||
| 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] | |
| -0.65 | -0.32 | -0.122 | 0.143 | -0.056 | 0.652 | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 31.154 |
| r_dihedral_angle_4_deg | 17.978 |
| r_dihedral_angle_3_deg | 12.114 |
| r_dihedral_angle_1_deg | 7.011 |
| r_lrange_it | 5.786 |
| r_rigid_bond_restr | 3.001 |
| r_lrange_other | 2.52 |
| r_scangle_it | 2.377 |
| r_angle_refined_deg | 2.288 |
| r_scangle_other | 2.208 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| Sample |
|---|
| Lysozyme |
| 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) | |
| Resolution Method | DIFFRACTION PATTERN/LAYERLINES |
| Other Details | |
| Refinement Type | |
| Symmetry Type | 3D CRYSTAL |
| Space Group Name | |
| Length a | 26.42 |
| Length b | 30.72 |
| Length c | 30.72 |
| Angle Alpha | 112.075 |
| Angle Beta | 109.095 |
| Angle Gamma | 112.075 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | RECIPROCAL | ||||
| Refinement Protocol | AB INITIO MODEL | ||||
| Refinement Target | Maximum likelihood | ||||
| Overall B Value | 12.188 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON IV (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 0.001 | ||||||||
| 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 | 2.7 |
| 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 REFINEMENT | REFMAC | |
| CRYSTALLOGRAPHY MERGING | AIMLESS | |
| RECONSTRUCTION | REFMAC | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| NONE | ||||
