7Z59

SARS-CoV-2 main protease (Mpro) covalently modified with a penicillin derivative


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6293SARS-CoV-2 Mpro was thawed and diluted to 6 mg/mL (using 20 mM HEPES, pH 7.5, 50 mM NaCl). Beta-Lactam 20e was added to the protein solution to a final concentration of 10 mM; the mixture was incubated for 2 h at ambient temperature prior to dispensing plates. The drop composition was 0.15 uL protein ligand solution, 0.3 uL 11 percent v/v PEG 4000, 0.1 M MES, pH 6.5, and 0.05 ,microL Mpro crystal seed stock. The Mpro crystal seed stock was prepared by crushing Mpro crystals with a pipette tip, suspending them in 30% PEG 4000, 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). As reservoir solution was used: 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 degree C and appeared within 24 h, reaching full size within 36 h. Crystals were looped after one week.
Crystal Properties
Matthews coefficientSolvent content
1.9938.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.341α = 90
b = 53.808β = 100.649
c = 44.703γ = 90
Symmetry
Space GroupC 1 2 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 I030.97625DiamondI03

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
1255.6951000.1880.2080.0880.9977.910.718025
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)
122.051004.0664.491.8930.21110.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6yb7255.6951801788399.9780.2240.22230.251648.528
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]
0.378-0.0240.305-0.629
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.145
r_dihedral_angle_3_deg13.828
r_dihedral_angle_4_deg10.944
r_dihedral_angle_1_deg10.656
r_lrange_it9.864
r_lrange_other9.863
r_scangle_it6.118
r_scangle_other6.117
r_mcangle_other4.93
r_mcangle_it4.927
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.145
r_dihedral_angle_3_deg13.828
r_dihedral_angle_4_deg10.944
r_dihedral_angle_1_deg10.656
r_lrange_it9.864
r_lrange_other9.863
r_scangle_it6.118
r_scangle_other6.117
r_mcangle_other4.93
r_mcangle_it4.927
r_scbond_it4.251
r_scbond_other4.249
r_mcbond_it3.345
r_mcbond_other3.33
r_angle_refined_deg1.481
r_angle_other_deg1.37
r_symmetry_nbd_refined0.258
r_nbd_refined0.21
r_nbd_other0.2
r_ext_dist_refined_d0.193
r_xyhbond_nbd_refined0.193
r_symmetry_nbd_other0.18
r_nbtor_refined0.174
r_symmetry_xyhbond_nbd_other0.169
r_symmetry_xyhbond_nbd_refined0.149
r_symmetry_nbtor_other0.075
r_chiral_restr0.063
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2358
Nucleic Acid Atoms
Solvent Atoms131
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
BUSTERrefinement
Aimlessdata scaling
xia2data reduction
MOLREPphasing