7UUG
SARS-CoV-2 Main Protease S144A (Mpro S144A) in Complex with ML1006a
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 289.15 | Sitting drops consisted of 0.19 uL A:0.19 uL B: A) 5.1 mg/mL Mpro S144A + 0.9 mM ML1006a in in 20 mM Tris pH 7.3 + 3 mM TCEP + 3 % DMSO B) 0.1 M MES pH 6.5, 10% PEG20000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.24 | 45.09 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 63.613 | α = 90 |
b = 45.462 | β = 90 |
c = 104.749 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 PILATUS 6M | Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2 | 2022-03-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL12-2 | 0.97946 | SSRL | BL12-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (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 | 104.749 | 99.9 | 0.061 | 0.067 | 0.026 | 13.2 | 6.7 | 21242 | 21242 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2 | 2.11 | 100 | 1.269 | 1.269 | 1.374 | 0.521 | 0.6 | 6.9 |
Refinement
Statistics | |||||||||||||||||||
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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 | 6LZE | 2 | 34.94 | 20152 | 1066 | 99.88 | 0.1853 | 0.1824 | 0.2404 | RANDOM | 49.11 |
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] | |
2.59 | -1.96 | -0.62 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.431 |
r_dihedral_angle_3_deg | 15.514 |
r_dihedral_angle_4_deg | 14.104 |
r_dihedral_angle_1_deg | 7.659 |
r_angle_refined_deg | 1.591 |
r_angle_other_deg | 1.312 |
r_chiral_restr | 0.067 |
r_bond_refined_d | 0.008 |
r_gen_planes_refined | 0.007 |
r_bond_other_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2366 |
Nucleic Acid Atoms | |
Solvent Atoms | 68 |
Heterogen Atoms | 42 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
PHASER | phasing |
PDB_EXTRACT | data extraction |