7NT2
Crystal structure of SARS CoV2 main protease in complex with FSP006
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6LU7 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | 0.1 M MES pH 6.5 15% w/v PEG 6000 5% v/v MPD Compound stock FSP006 100 mM in 100% DMSO Crystals were soaked for 3 hours with final concentration of 10 mM FSP006 by adding the stock to crystallisation drops in a 1/10 ratio yielding 10% (V/V) final DMSO concentration. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.65545678 | 53.7090645 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 68.155 | α = 90 |
b = 100.588 | β = 90 |
c = 104.726 | 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 EIGER X 16M | 2020-11-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 1.000035 | SLS | X06SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 2.14 | 46.45 | 98.1 | 0.132 | 0.149 | 0.069 | 0.997 | 9.8 | 7.8 | 39260 |
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) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.14 | 2.21 | 1.329 | 1.516 | 0.712 | 0.634 | 7.9 |
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 (All) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 6lu7 | 2.145 | 46.447 | 39220 | 1962 | 97.657 | 0.204 | 0.2019 | 0.2514 | RANDOM | 40.003 |
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] | |
-2.693 | 2.82 | -0.127 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35 |
r_dihedral_angle_4_deg | 16.876 |
r_dihedral_angle_3_deg | 15.942 |
r_dihedral_angle_1_deg | 7.942 |
r_lrange_it | 7.812 |
r_lrange_other | 7.783 |
r_scangle_it | 5.54 |
r_scangle_other | 5.539 |
r_mcangle_it | 4.662 |
r_mcangle_other | 4.661 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4681 |
Nucleic Acid Atoms | |
Solvent Atoms | 179 |
Heterogen Atoms | 61 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
REFMAC | refinement |
Aimless | data reduction |
XDS | data processing |
Aimless | data scaling |
PHASER | phasing |
Coot | model building |