8DZA

Crystal Structure of SARS-CoV-2 Main protease A193T 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% v/v DMSO, 8% w/v PEG4000, 30% w/v PEG400
Crystal Properties
Matthews coefficientSolvent content
2.652.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.989α = 90
b = 99.979β = 90
c = 103.638γ = 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 SIRIUS BEAMLINE MANACA0.977180LNLS SIRIUSMANACA

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
11.9672.0658.70.9917.87.829962
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)
11.962.030.253

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-VALUE7mbg1.96172.05829962145858.320.2030.20070.241934.182
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]
0.0120.189-0.201
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.765
r_dihedral_angle_4_deg19.574
r_dihedral_angle_3_deg15.479
r_lrange_it7.912
r_lrange_other7.905
r_dihedral_angle_1_deg7.68
r_scangle_it4.428
r_scangle_other4.428
r_mcangle_it3.458
r_mcangle_other3.458
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.765
r_dihedral_angle_4_deg19.574
r_dihedral_angle_3_deg15.479
r_lrange_it7.912
r_lrange_other7.905
r_dihedral_angle_1_deg7.68
r_scangle_it4.428
r_scangle_other4.428
r_mcangle_it3.458
r_mcangle_other3.458
r_scbond_it2.81
r_scbond_other2.81
r_mcbond_it2.15
r_mcbond_other2.147
r_angle_refined_deg1.417
r_angle_other_deg1.282
r_nbd_other0.339
r_symmetry_xyhbond_nbd_refined0.32
r_symmetry_xyhbond_nbd_other0.318
r_symmetry_nbd_refined0.277
r_xyhbond_nbd_refined0.22
r_nbd_refined0.206
r_symmetry_nbd_other0.202
r_nbtor_refined0.165
r_symmetry_nbtor_other0.079
r_chiral_restr0.061
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4691
Nucleic Acid Atoms
Solvent Atoms175
Heterogen Atoms90

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing