9GV2 | pdb_00009gv2

Crystal structure of SARS-CoV-2 main protease (MPro) in complex with the covalently bound inhibitor FP237 (compound 8p in publication)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2980.1M MMT (sodium malonate, imidazole, and boric acid in the molar ratios 2:3:3), pH 5.0, 25% w/v polyethylene glycol (PEG)1500
Crystal Properties
Matthews coefficientSolvent content
2.0740.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.183α = 90
b = 54.817β = 100.49
c = 115.091γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2023-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.9762PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.56113.1772.40.2470.1190.9876.24.913198
Highest Resolution Shell
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)RedundancyNumber Unique Reflections (All)
12.562.771.2150.6280.4841.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)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)Mean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISFREE R-VALUE2.56113.171.351318768972.370.22550.22260.22650.28090.2806
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_d14.369
f_angle_d0.765
f_chiral_restr0.047
f_plane_restr0.008
f_bond_d0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4682
Nucleic Acid Atoms
Solvent Atoms12
Heterogen Atoms104

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
STARANISOdata scaling
PHENIXphasing