Joint neutron/X-ray structure of SARS-CoV-2 3CL Mpro at room temperature
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 6WQF | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, SITTING DROP | | 287 | 18% PEG3350, 0.1 M Bis-Tris pH 6.6, 3% DMSO |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.06 | 40.25 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 114.927 | α = 90 |
| b = 54.686 | β = 101.46 |
| c = 45.216 | 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 | | 2020-07-20 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 293 | AREA DETECTOR | ORNL ANGER CAMERA | | 2020-07-15 | L | LAUE |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.54 | | |
| 2 | SPALLATION SOURCE | ORNL Spallation Neutron Source BEAMLINE MANDI | 2.0-4.0 | 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 | 2.3 | 56.32 | 97.9 | 0.129 | | | 0.07 | 0.991 | | 9.31 | 4.3 | | 12094 | | | |
| 1 | 2.5 | 14.95 | 83.9 | 0.19 | | | | | | 13 | 5.7 | | 8031 | | | |
| 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 | 2.3 | 2.38 | | 0.589 | | | 0.355 | 0.5 | | 1.6 | 3.7 | |
| 1 | 2.5 | 2.59 | | 0.333 | | | | | | 3.7 | 4.7 | |
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 2.3 | 28.16 | | | | 10179 | 537 | 82.4 | | | 0.185 | 0.17 | 0.22 | 0.2 | | 40.27 |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2.5 | 14.96 | | | | 8018 | 413 | 83.5 | | | 0.201 | | 0.253 | | | 40.27 |
| 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 |
|---|
| x_torsion_deg | 17.7 |
| x_torsion_deg | 17.7 |
| x_angle_deg | 1.1 |
| x_angle_deg | 1.1 |
| x_torsion_impr_deg | 1 |
| x_torsion_impr_deg | 1 |
| x_bond_d | 0.008 |
| x_bond_d | 0.008 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 2368 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 66 |
| Heterogen Atoms | |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| nCNS | refinement |
| PHASER | phasing |
| CrysalisPro | data reduction |
| CrysalisPro | data scaling |
| Mantid | data reduction |
| Mantid | data scaling |
