8DCZ

Crystal Structure of SARS-CoV-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293.150.2M Sodium Chloride, 10% 1-6HexD, 20% PEG MME 2000
Crystal Properties
Matthews coefficientSolvent content
2.0439.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.566α = 90
b = 53.786β = 100.53
c = 114.76γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2022-06-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.385098.60.09212.33421947
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.382.420.4812.13

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT7LYH2.3839.2820252112496.020.19490.19190.2513RANDOM37.611
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]
1.26-0.69-0.65-0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.021
r_dihedral_angle_2_deg12.304
r_dihedral_angle_1_deg7.981
r_angle_refined_deg1.238
r_angle_other_deg0.428
r_chiral_restr0.057
r_gen_planes_refined0.006
r_bond_refined_d0.005
r_bond_other_d0.005
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4724
Nucleic Acid Atoms
Solvent Atoms140
Heterogen Atoms70

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing