7MRR

Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) in Complex with Covalent Inhibitor Leupeptin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7NEV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293PEG 4000, HEPES pH 7.0, 3% DMSO
Crystal Properties
Matthews coefficientSolvent content
238.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.186α = 90
b = 53.181β = 102.24
c = 45.917γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-03-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS-II BEAMLINE 17-ID-20.9793NSLS-II17-ID-2

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
12.3227.6798.30.1150.1260.0510.99712.16.411449
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)
12.322.3879.21.0811.1860.4810.6365.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT7NEV2.3227.651093951098.280.19640.1940.2455RANDOM57.256
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]
3.90.41-2.98-1.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.787
r_dihedral_angle_3_deg15.519
r_dihedral_angle_4_deg15.426
r_dihedral_angle_1_deg8.074
r_angle_other_deg2.401
r_angle_refined_deg1.537
r_chiral_restr0.062
r_bond_other_d0.035
r_gen_planes_refined0.009
r_gen_planes_other0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.787
r_dihedral_angle_3_deg15.519
r_dihedral_angle_4_deg15.426
r_dihedral_angle_1_deg8.074
r_angle_other_deg2.401
r_angle_refined_deg1.537
r_chiral_restr0.062
r_bond_other_d0.035
r_gen_planes_refined0.009
r_gen_planes_other0.009
r_bond_refined_d0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2367
Nucleic Acid Atoms
Solvent Atoms38
Heterogen Atoms46

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing