7Z4S

Crystal structure of SARS-CoV-2 Mpro in complex with cyclic peptide GM4 including unnatural amino acids.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6YB7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6293Mpro was thawed and diluted to 6 mg/ml using 20 mM Hepes pH 7.5, 50 mM NaCl. GM4 was diluted into the protein solution to a final concentration of 10 mM and allowed to incubate 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 11% (v/v) PEG 4K, 5% (v/v) DMSO, 0.1 M MES pH 6.5. Crystals were grown using the sitting drop vapor diffusion method at 20 C and appeared within 24 hours, reaching full size within 36 hours. Crystals were looped after one week.
Crystal Properties
Matthews coefficientSolvent content
2.3447.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.515α = 113.87
b = 56.112β = 110.53
c = 63.238γ = 90.92
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-12-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9762DiamondI03

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
11.753.2399.90.1290.0580.9986.65.9407784
Highest Resolution Shell
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)RedundancyNumber Unique Reflections (All)
11.71.7399.22.4543.0590.2980.6

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 REPLACEMENTTHROUGHOUT6yb71.753.2365737336699.580.199850.19820.23379RANDOM36.483
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]
-1.35-0.4-0.450.320.250.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.997
r_dihedral_angle_4_deg14.606
r_dihedral_angle_3_deg13.08
r_long_range_B_refined7.246
r_long_range_B_other7.239
r_dihedral_angle_1_deg6.492
r_scangle_other4.848
r_scbond_it3.432
r_scbond_other3.432
r_mcangle_it2.973
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.997
r_dihedral_angle_4_deg14.606
r_dihedral_angle_3_deg13.08
r_long_range_B_refined7.246
r_long_range_B_other7.239
r_dihedral_angle_1_deg6.492
r_scangle_other4.848
r_scbond_it3.432
r_scbond_other3.432
r_mcangle_it2.973
r_mcangle_other2.973
r_mcbond_it2.239
r_mcbond_other2.238
r_angle_refined_deg1.322
r_angle_other_deg1.092
r_chiral_restr0.08
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4892
Nucleic Acid Atoms
Solvent Atoms292
Heterogen Atoms70

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing