9EOR
SARS-CoV2 major protease in complex with a covalent inhibitor SLL12.
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 7PFL | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 293 | 20% w/v PEG3350 0.2M potassium-thiocyanate 0.1M bis-tris propane pH 8.5 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.68 | 54.15 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 69.827 | α = 78.96 |
| b = 85.558 | β = 87.18 |
| c = 93.668 | γ = 83.17 |
| Symmetry | |
|---|---|
| Space Group | P 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 | 2021-09-18 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | MAX IV BEAMLINE BioMAX | 0.976254 | MAX IV | BioMAX |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 2.25 | 43.91 | 58.8 | 0.157 | 0.186 | 0.098 | 0.989 | 6.7 | 3.5 | 58705 | |||||||||
| 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) | ||||||||
| 1 | 2.25 | 2.44 | 13.9 | 0.683 | 0.812 | 0.433 | 0.597 | 1.8 | 3.4 | ||||||||||
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2.25 | 43.91 | 55787 | 2918 | 58.8 | 0.24322 | 0.24084 | 0.28912 | RANDOM | 33.558 | |||||||
| 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] | |
| 0.08 | 0.15 | 0.1 | 0.01 | -0.16 | -0.1 | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 17.505 |
| r_dihedral_angle_3_deg | 17.45 |
| r_long_range_B_refined | 9.77 |
| r_long_range_B_other | 9.77 |
| r_dihedral_angle_1_deg | 6.998 |
| r_scangle_other | 5.562 |
| r_mcangle_it | 5.103 |
| r_mcangle_other | 5.103 |
| r_scbond_it | 3.489 |
| r_scbond_other | 3.489 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 14262 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 347 |
| Heterogen Atoms | 145 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| STARANISO | data scaling |
| XDS | data reduction |
| PHASER | phasing |
