PanDDA analysis group deposition -- Main Protease (SARS-CoV-2) in complex with fragment G04 from the F2X-Entry Screen in orthorhombic space group
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7BB2 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.7 | 291 | 0.2 M MIB (sodium malonate, imidazole, and boric acid in the molar ratios 2:3:3) pH 7.7, 23.5 % PEG 1500, 5 % DMSO, 1 mM DTT. Crystal seeds were used to ensure reproducible crystal growth. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.57 | 52.1 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 67.69 | α = 90 |
b = 99.33 | β = 90 |
c = 103.18 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 PILATUS3 6M | 2022-12-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.9184 | BESSY | 14.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 1.77 | 45.78 | 99.7 | 0.11800000000000001 | 0.13 | 0.998 | 10.46 | 68400 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.77 | 1.88 | 99.6 | 1.6680000000000001 | 1.831 | 0.405 |
Refinement
Statistics | |||||||||||||||||||
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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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.77 | 45.78 | 66300 | 2100 | 99.6 | 0.21806 | 0.21676 | 0.2244 | 0.25995 | 0.2625 | RANDOM | 32.383 |
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] | |
-1.21 | 1.14 | 0.07 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 13.932 |
r_dihedral_angle_2_deg | 8.968 |
r_long_range_B_other | 7.579 |
r_long_range_B_refined | 7.576 |
r_dihedral_angle_1_deg | 7.186 |
r_scangle_other | 5.679 |
r_mcangle_it | 4.079 |
r_mcangle_other | 4.079 |
r_scbond_it | 3.528 |
r_scbond_other | 3.528 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4658 |
Nucleic Acid Atoms | |
Solvent Atoms | 139 |
Heterogen Atoms | 26 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data scaling |
XDS | data reduction |
PHASER | phasing |