7LBN
X-ray crystal structure of the SARS-CoV-2 main protease with Calpain I Inhibitor
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293 | 0.2M sodium citrate, 15% PEG3350, 20mM HEPES pH 7.5 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.78 | 55.7 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 97.481 | α = 90 |
| b = 80.729 | β = 114.36 |
| c = 51.579 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 1 2 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER X 16M | 2020-11-13 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | CHESS BEAMLINE A1 | 1 | CHESS | A1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | |||||||
| 1 | 1.76 | 50 | 97 | 0.038 | 0.905 | 38.4 | 3.2 | 35055 | 23.88 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 1 | 1.76 | 1.79 | 72.4 | 0.295 | 0.905 | 3.9 | 2.4 | ||||||||||||
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 6WTK | 1.76 | 43.25 | 33044 | 2000 | 97.69 | 0.16125 | 0.15979 | 0.18546 | RANDOM | 33.246 | ||||||
| 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] | |
| 0.02 | 0.2 | 0.15 | -0.25 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.999 |
| r_dihedral_angle_4_deg | 14.56 |
| r_dihedral_angle_3_deg | 12.148 |
| r_long_range_B_refined | 7.759 |
| r_long_range_B_other | 7.675 |
| r_dihedral_angle_1_deg | 6.895 |
| r_scangle_other | 3.683 |
| r_scbond_it | 2.608 |
| r_scbond_other | 2.6 |
| r_mcangle_it | 2.371 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2297 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 303 |
| Heterogen Atoms | 32 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| HKL-2000 | data scaling |
| HKL-2000 | data reduction |
| PHASER | phasing |
| REFMAC | refinement |
