7MLF

Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) Covalently Bound to Compound C7


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6Y2EPDB entry 6Y2E

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29530% PEG2000 MME, 0.1 M potassium thiocyanate
Crystal Properties
Matthews coefficientSolvent content
2.0941.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.81α = 90
b = 53.54β = 98.92
c = 45.33γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2021-02-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08B1-11.52131CLSI08B1-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.638.493.180.99661.98666
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.69348.820.6790.451.9

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 REPLACEMENTTHROUGHOUTPDB entry 6Y2E2.638.4810344398.630.223390.220360.27853RANDOM60.609
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]
3.43-1.21-1.7-1.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.856
r_dihedral_angle_4_deg19.531
r_dihedral_angle_3_deg14.085
r_dihedral_angle_1_deg6.73
r_long_range_B_refined5.479
r_long_range_B_other5.475
r_mcangle_it3.07
r_mcangle_other3.07
r_scangle_other2.797
r_mcbond_it1.752
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.856
r_dihedral_angle_4_deg19.531
r_dihedral_angle_3_deg14.085
r_dihedral_angle_1_deg6.73
r_long_range_B_refined5.479
r_long_range_B_other5.475
r_mcangle_it3.07
r_mcangle_other3.07
r_scangle_other2.797
r_mcbond_it1.752
r_mcbond_other1.749
r_scbond_it1.562
r_scbond_other1.561
r_angle_refined_deg1.22
r_angle_other_deg1.059
r_chiral_restr0.038
r_gen_planes_refined0.003
r_bond_refined_d0.002
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2347
Nucleic Acid Atoms
Solvent Atoms40
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing