7AEG

SARS-CoV-2 main protease in a covalent complex with SDZ 224015 derivative, compound 5


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5R8T 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293Mpro was thawed and diluted to 6 mg/ml using 20 mM Hepes pH 7.5, 50 mM NaCl. The ligand of interest was dissolved in DMSO to 10 mM and then diluted into the protein solution to a final concentration of 1 mM. The ligand was then allowed to incubate with the protein for two hours at room temperature prior to dispensing plates. The drop composition was 0.15 ul protein ligand solution, 0.3 ul 11% (v/v) PEG 4K, 0.1 M MES pH 6.5, and 0.05 ul Mpro crystal seed stock. The Mpro crystal seed stock was prepared by crushing Mpro crystals with a pipette tip, suspending them in 30% PEG 4K, 5% (v/v) DMSO, 0.1 M MES pH 6.5, and vortexing for 60 s with approximately 10 glass beads (1.0 mm diameter, BioSpec products). Reservoir solution was 11pc (v/v) PEG 4K, 5pc (v/v) DMSO, 0.1 M MES pH 6.5. Crystals were grown using the sitting drop vapor diffusion method at 20 degrees C and appeared within 24 hours, reaching full size within 36 hours.
Crystal Properties
Matthews coefficientSolvent content
1.9336.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.871α = 90
b = 52.939β = 103.05
c = 45.526γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2020-07-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.999DiamondI24

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
11.754.9899.90.2240.2450.0990.9857.66.228892
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)
11.71.7399.82.9273.2271.3360.3016

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5r8t1.754.9827473141899.860.1660.16410.2021RANDOM18.033
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]
0.39-0.18-0.420.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.966
r_dihedral_angle_4_deg13.144
r_dihedral_angle_3_deg12.29
r_dihedral_angle_1_deg7.036
r_angle_refined_deg1.375
r_angle_other_deg1.337
r_chiral_restr0.068
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.966
r_dihedral_angle_4_deg13.144
r_dihedral_angle_3_deg12.29
r_dihedral_angle_1_deg7.036
r_angle_refined_deg1.375
r_angle_other_deg1.337
r_chiral_restr0.068
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2359
Nucleic Acid Atoms
Solvent Atoms192
Heterogen Atoms82

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
DIALSdata reduction
xia2data reduction
MOLREPphasing