Joint X-ray/neutron structure of SARS-CoV-2 main protease (3CL Mpro) in complex with Telaprevir
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 6XQS | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, SITTING DROP | 6.6 | 287 | 18% PEG3350, 0.1 M Bis-Tris pH 6.6 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.18 | 43.52 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 110.558 | α = 90 |
| b = 55.691 | β = 101.31 |
| c = 48.808 | 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 | 293 | PIXEL | DECTRIS EIGER R 4M | | 2020-10-20 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 293 | AREA DETECTOR | ORNL ANGER CAMERA | | 2020-10-15 | L | LAUE |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 | | |
| 2 | SPALLATION SOURCE | ORNL Spallation Neutron Source BEAMLINE MANDI | 2.0 - 4.16 | ORNL Spallation Neutron Source | MANDI |
Data Collection
| Overall |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | 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 | 54.21 | 96.3 | 0.082 | | | | | | 13.9 | 4.2 | | 19852 | | | |
| 2 | 2.4 | 14.29 | 83.4 | 0.176 | | | | | | 11.4 | 4.05 | | 9566 | | | |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 2 | 2.05 | | 0.544 | | | | | | 1.9 | 4 | |
| 2 | 2.4 | 2.49 | | 0.336 | | | | | | 3.1 | 2.68 | |
Refinement
| Statistics |
|---|
| Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 2 | 40 | | 2.5 | | 19261 | 984 | 97.5 | | | 0.204 | 0.225 | RANDOM | 38.51 |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2.4 | 14.92 | | 2.5 | | 9539 | 470 | 82.8 | | | 0.216 | 0.228 | RANDOM | |
| 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 |
|---|
| o_angle_deg | 1.1 |
| o_bond_d | 0.009 |
| o_bond_d_na | |
| o_bond_d_prot | |
| o_angle_d | |
| o_angle_d_na | |
| o_angle_d_prot | |
| o_angle_deg_na | |
| o_angle_deg_prot | |
| o_dihedral_angle_d | |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| o_angle_deg | 1.1 |
| o_bond_d | 0.009 |
| o_bond_d_na | |
| o_bond_d_prot | |
| o_angle_d | |
| o_angle_d_na | |
| o_angle_d_prot | |
| o_angle_deg_na | |
| o_angle_deg_prot | |
| o_dihedral_angle_d | |
| o_dihedral_angle_d_na | |
| o_dihedral_angle_d_prot | |
| o_improper_angle_d | |
| o_improper_angle_d_na | |
| o_improper_angle_d_prot | |
| o_mcbond_it | |
| o_mcangle_it | |
| o_scbond_it | |
| o_scangle_it | |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 2368 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 95 |
| Heterogen Atoms | 49 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| nCNS | refinement |
| PHASER | phasing |
| CrysalisPro | data reduction |
| CrysalisPro | data scaling |
| Mantid | data reduction |
| LAUENORM | data scaling |
