7BIJ

Crystal Structure of SARS-CoV-2 main protease (Nsp5) in complex with compound 13


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7B2J 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.75293100 nL protein (8.3 mg/mL, 50 mM Tris pH 8.0, 300 mM NaCl), 50 nL seeds, 450 nL reservoir (200 mM HEPES pH 7.75, 5% DMSO, 12.5% PEG4K). Soaking: 200 mM HEPES pH 7.75, 12.5 mM compound, 5% DMSO, 10% PEG300, 20% PEG3K, RT, 2 h.
Crystal Properties
Matthews coefficientSolvent content
238.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.745α = 90
b = 53.839β = 100.584
c = 44.589γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-12-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX IV BEAMLINE BioMAX0.97625MAX IVBioMAX

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
11.4733.9398.50.0580.0690.0370.99813.76.544811
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)
11.471.585.40.4590.5230.3720.8392.44.4

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-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE7B2J1.4733.9344811218398.3650.1770.17540.2125Random selection24.61
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]
1.524-0.643-0.185-1.027
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.242
r_dihedral_angle_4_deg16.744
r_dihedral_angle_3_deg11.932
r_dihedral_angle_1_deg7.075
r_lrange_it6.158
r_scangle_it4.835
r_scbond_it3.465
r_mcangle_it3.014
r_mcbond_it2.129
r_angle_refined_deg1.799
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.242
r_dihedral_angle_4_deg16.744
r_dihedral_angle_3_deg11.932
r_dihedral_angle_1_deg7.075
r_lrange_it6.158
r_scangle_it4.835
r_scbond_it3.465
r_mcangle_it3.014
r_mcbond_it2.129
r_angle_refined_deg1.799
r_nbtor_refined0.322
r_symmetry_xyhbond_nbd_refined0.219
r_symmetry_nbd_refined0.215
r_nbd_refined0.213
r_xyhbond_nbd_refined0.162
r_chiral_restr0.12
r_gen_planes_refined0.012
r_bond_refined_d0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2358
Nucleic Acid Atoms
Solvent Atoms322
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing