8E1Y

Crystal Structure of SARS-CoV-2 Main protease A193S 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 DIFFUSION2930.1 M MES pH 6.7, 5% DMSO, 8% PEG 4000 Cryo protected with 40% PEG 400
Crystal Properties
Matthews coefficientSolvent content
2.6353.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.905α = 90
b = 103.925β = 90
c = 68.025γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2022-04-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS SIRUS BEAMLINE MANACA0.977180LNLS 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
12.4872.559.50.9653.96.415497
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)
12.482.570.575

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-VALUE7mbg2.4872.51548176559.5060.2190.21660.272331.165
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]
0.386-0.336-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.677
r_dihedral_angle_4_deg19.976
r_dihedral_angle_3_deg17.156
r_dihedral_angle_1_deg7.569
r_lrange_it5.647
r_lrange_other5.647
r_mcangle_it3.175
r_mcangle_other3.174
r_scangle_it2.896
r_scangle_other2.896
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.677
r_dihedral_angle_4_deg19.976
r_dihedral_angle_3_deg17.156
r_dihedral_angle_1_deg7.569
r_lrange_it5.647
r_lrange_other5.647
r_mcangle_it3.175
r_mcangle_other3.174
r_scangle_it2.896
r_scangle_other2.896
r_mcbond_it1.781
r_mcbond_other1.781
r_scbond_it1.638
r_scbond_other1.637
r_angle_refined_deg1.487
r_angle_other_deg1.301
r_nbd_other0.538
r_symmetry_nbd_refined0.504
r_symmetry_xyhbond_nbd_other0.414
r_symmetry_nbd_other0.208
r_nbd_refined0.2
r_xyhbond_nbd_refined0.197
r_nbtor_refined0.166
r_symmetry_xyhbond_nbd_refined0.147
r_symmetry_nbtor_other0.08
r_chiral_restr0.057
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4669
Nucleic Acid Atoms
Solvent Atoms31
Heterogen Atoms78

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing