7K6E
SARS-CoV-2 Main Protease Co-Crystal Structure with Telaprevir Determined from Crystals Grown with 40 nL Acoustically Ejected Mpro Droplets at 1.63 A Resolution (Direct Vitrification)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7JYC |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 293 | 22% PEG 4000, 100 mM HEPES pH 7.0, 3% DMSO |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.1 | 41.32 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 109.6 | α = 90 |
b = 54.71 | β = 101.231 |
c = 48.04 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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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 9M | 2020-08-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS-II BEAMLINE 17-ID-1 | 0.92 | NSLS-II | 17-ID-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.63 | 53.75 | 100 | 0.136 | 0.044 | 0.998 | 9.2 | 10.3 | 34940 | 28.65 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.63 | 1.66 | 99.9 | 3.347 | 1.091 | 0.368 | 0.7 | 10.3 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 7JYC | 1.63 | 53.75 | 1.34 | 34931 | 2000 | 99.95 | 0.2159 | 0.2141 | 0.2453 | 36.06 |
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 | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 17.57 |
f_angle_d | 0.8997 |
f_chiral_restr | 0.048 |
f_bond_d | 0.0069 |
f_plane_restr | 0.0067 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2330 |
Nucleic Acid Atoms | |
Solvent Atoms | 54 |
Heterogen Atoms | 53 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
AutoProcess | data reduction |
XDS | data reduction |
XSCALE | data scaling |
Aimless | data processing |
pointless | data processing |
PHASER | phasing |