8E26

Crystal Structure of SARS-CoV-2 Main Protease N142S mutant in complex with Nirmatrelvir


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M MES, pH 6.7, 5% v/v DMSO, 8% w/v PEG4000, 30% w/v PEG400
Crystal Properties
Matthews coefficientSolvent content
2.6152.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.841α = 90
b = 100.619β = 90
c = 103.356γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS PILATUS 2M2022-05-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS SIRUS BEAMLINE MANACA0.9772LNLS SIRUSMANACA

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
11.84556.31339.620.9494.4424397
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)
11.8452.20710.20.8231.5

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE7MBG1.84556.31324393119239.6320.2260.22420.265417.926
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]
0.5360.203-0.738
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.53
r_dihedral_angle_4_deg18.586
r_dihedral_angle_3_deg16.447
r_dihedral_angle_1_deg7.152
r_lrange_it4.11
r_lrange_other4.059
r_mcangle_other2.077
r_mcangle_it2.075
r_scangle_it1.892
r_scangle_other1.892
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.53
r_dihedral_angle_4_deg18.586
r_dihedral_angle_3_deg16.447
r_dihedral_angle_1_deg7.152
r_lrange_it4.11
r_lrange_other4.059
r_mcangle_other2.077
r_mcangle_it2.075
r_scangle_it1.892
r_scangle_other1.892
r_angle_refined_deg1.289
r_angle_other_deg1.268
r_mcbond_it1.172
r_mcbond_other1.161
r_scbond_it1.065
r_scbond_other1.064
r_symmetry_xyhbond_nbd_refined0.381
r_nbd_other0.228
r_xyhbond_nbd_refined0.226
r_symmetry_nbd_refined0.218
r_symmetry_nbd_other0.201
r_nbd_refined0.192
r_nbtor_refined0.162
r_symmetry_xyhbond_nbd_other0.157
r_symmetry_nbtor_other0.078
r_chiral_restr0.054
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4732
Nucleic Acid Atoms
Solvent Atoms219
Heterogen Atoms78

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing