7B83

Structure of SARS-CoV-2 Main Protease bound to pyrithione zinc


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7AR6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1COUNTER-DIFFUSION291Co-crystallization with the compounds was achieved mixing 0.23 uL of protein solution (6.25 mg/mL) in 20 mM HEPES buffer (pH 7.8) containing 1 mM DTT/TCEP (respectively), 1 mM EDTA, and 150 mM NaCl with 0.22 uL of reservoir solution consisting of 100 mM MIB, pH 7.5, containing 25% w/w PEG 1500 and 5% (v/v) DMSO, and 0.05 uL of a micro-seed crystal suspension. This growth solution was equilibrated by sitting drop vapor diffusion against 40 uL reservoir solution. Prior to crystallization 125 nL droplets of 10 mM compound solutions from the two libraries in DMSO were applied to the wells of SwissCI 96-well plates (2-well or 3-well low profile, respectively) and subsequently dried in vacuum. Taking the crystallization drop volume into account this resulted in a final compound concentration of 2.5 mM and a molar ratio of 13.6 of compound to protein. To obtain well-diffracting crystals in a reproducible way micro-seeding was applied for crystal growth. Crystals appeared within a few hours and reached their final size (200x100x10 um3) after 2 - 3 days. Crystals were manually harvested and flash-frozen in liquid nitrogen for subsequent X-ray diffraction data collection.
Crystal Properties
Matthews coefficientSolvent content
1.9536.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.357α = 90
b = 53.113β = 102.982
c = 44.891γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-04-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P111.0332PETRA III, DESYP11

Data Collection

Overall
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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.847.8799.40.1070.1230.060.9978.842418926.99
Highest Resolution Shell
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)RedundancyNumber Unique Reflections (All)
11.81.8394.22.1872.5271.2450.2610.63.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE7AR61.823.931.342412381299.510.18490.18410.206731.85
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d17.8736
f_angle_d0.7533
f_chiral_restr0.0511
f_bond_d0.0102
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2360
Nucleic Acid Atoms
Solvent Atoms280
Heterogen Atoms19

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing