7NBT

Crystal Structure of SARS-CoV-2 main protease (Nsp5) in complex with compound 21


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
1.9938.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.582α = 90
b = 53.77β = 100.526
c = 44.524γ = 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
11.6356.3398.10.060.0740.0430.99811.15.132705
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)
11.631.660.7470.9320.550.77425.1

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-VALUE7B2J1.6343.81332700162198.0270.1920.19040.2302Random selection29.495
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]
3.130.059-1.231-1.797
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.217
r_dihedral_angle_3_deg14.156
r_dihedral_angle_4_deg9.985
r_dihedral_angle_1_deg7.127
r_lrange_it6.49
r_scangle_it5.093
r_scbond_it3.67
r_mcangle_it3.224
r_mcbond_it2.421
r_angle_refined_deg1.552
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.217
r_dihedral_angle_3_deg14.156
r_dihedral_angle_4_deg9.985
r_dihedral_angle_1_deg7.127
r_lrange_it6.49
r_scangle_it5.093
r_scbond_it3.67
r_mcangle_it3.224
r_mcbond_it2.421
r_angle_refined_deg1.552
r_nbtor_refined0.321
r_nbd_refined0.212
r_symmetry_nbd_refined0.209
r_xyhbond_nbd_refined0.159
r_symmetry_xyhbond_nbd_refined0.125
r_chiral_restr0.107
r_gen_planes_refined0.01
r_bond_refined_d0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2358
Nucleic Acid Atoms
Solvent Atoms149
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing