6ZET
Crystal structure of proteinase K nanocrystals by electron diffraction with a 20 micrometre C2 condenser aperture
ELECTRON CRYSTALLOGRAPHY
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 67.365 | α = 90 |
| b = 67.365 | β = 90 |
| c = 106.784 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 43 21 2 |
Data Collection
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 2.7 | 2.83 | 83.6 | 1.275 | 1.389 | 0.533 | 0.498 | 1.8 | 10.5 | |||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Work | R-Free | Mean Isotropic B | |||||||
| ELECTRON CRYSTALLOGRAPHY | MOLECULAR REPLACEMENT | FREE R-VALUE | 2ID8 | 2.701 | 57.04 | 6184 | 297 | 85.925 | 0.227 | 0.2247 | 0.2679 | 7.281 | |||||||
| 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] | |
| -0.134 | -0.134 | 0.267 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.442 |
| r_dihedral_angle_4_deg | 19.975 |
| r_dihedral_angle_3_deg | 16.12 |
| r_scangle_it | 5.536 |
| r_lrange_it | 5.499 |
| r_dihedral_angle_1_deg | 5.026 |
| r_scbond_it | 4.897 |
| r_mcangle_it | 3.796 |
| r_mcbond_it | 2.992 |
| r_angle_refined_deg | 1.207 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| DIALS | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
| Sample |
|---|
| proteinase K |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | 3D ARRAY |
| Vitrification Instrument | |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Excess liquid was removed by blotting for 4-6s with a Vitrobot |
| 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 | 67.3653 |
| Length b | 67.3653 |
| Length c | 67.3653 |
| Angle Alpha | 90 |
| Angle Beta | 90 |
| Angle Gamma | 90 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (2ID8) | ||||
| Refinement Space | RECIPROCAL | ||||
| Refinement Protocol | |||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | OTHER | OTHER | OTHER | OTHER | OTHER | OTHER | OTHER | OTHER | |
| Electron Dose (electrons/Å**2) | 0.034 | 0.034 | 0.034 | 0.034 | 0.034 | 0.034 | 0.034 | 0.034 | |
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | 2018-04-20 |
| Temperature (Kelvin) | |
| Microscope Model | FEI TALOS ARCTICA |
| Minimum Defocus (nm) | |
| Maximum Defocus (nm) | |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | DIFFRACTION |
| Specimen Holder Model | |
| Nominal Magnification | |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 200 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| MOLECULAR REPLACEMENT | Phaser | 2.8.2 |
| SYMMETRY DETERMINATION | POINTLESS | 1.11.12 |
| CRYSTALLOGRAPHY MERGING | AIMLESS | 0.7.1 |
| MODEL REFINEMENT | REFMAC | 5.8.0258 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
