7RN1

Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor Jun9-62-2R


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7KX5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29325% PEG 3350, 0.2 M AmSO4, 0.1 M HEPES 7.5
Crystal Properties
Matthews coefficientSolvent content
1.9938.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.27α = 90
b = 53.26β = 102.82
c = 45.46γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-04-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-ID

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
12.348.176.70.0880.1040.0520.9937.22.99032
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)
12.32.3882.20.4230.4950.250.7362.9

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 REPLACEMENTTHROUGHOUT7KX52.348859843475.230.19920.1980.2225RANDOM41.024
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]
0.76-0.210.25-0.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.117
r_dihedral_angle_3_deg15.899
r_dihedral_angle_4_deg14.507
r_dihedral_angle_1_deg7.904
r_angle_refined_deg1.544
r_angle_other_deg1.279
r_chiral_restr0.063
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.117
r_dihedral_angle_3_deg15.899
r_dihedral_angle_4_deg14.507
r_dihedral_angle_1_deg7.904
r_angle_refined_deg1.544
r_angle_other_deg1.279
r_chiral_restr0.063
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2352
Nucleic Acid Atoms
Solvent Atoms7
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
MOLREPphasing