8DZ6

Crystal Structure of SARS-CoV-2 Main protease mutant Q189K 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
2.6353.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.782α = 90
b = 101.572β = 90
c = 103.561γ = 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
12.36672.5256.90.9974.65.316996
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)
12.3662.450.683

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-VALUE7mbg2.36672.51516996170056.9060.2350.22860.296131.972
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]
-0.1940.236-0.042
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.56
r_dihedral_angle_4_deg25.075
r_dihedral_angle_3_deg16.796
r_dihedral_angle_1_deg7.801
r_lrange_other4.714
r_lrange_it4.698
r_scangle_it2.715
r_scangle_other2.714
r_mcangle_it2.701
r_mcangle_other2.701
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.56
r_dihedral_angle_4_deg25.075
r_dihedral_angle_3_deg16.796
r_dihedral_angle_1_deg7.801
r_lrange_other4.714
r_lrange_it4.698
r_scangle_it2.715
r_scangle_other2.714
r_mcangle_it2.701
r_mcangle_other2.701
r_scbond_it1.588
r_scbond_other1.588
r_mcbond_it1.578
r_mcbond_other1.577
r_angle_refined_deg1.388
r_angle_other_deg1.316
r_symmetry_xyhbond_nbd_refined0.486
r_nbd_other0.379
r_symmetry_nbd_refined0.372
r_symmetry_xyhbond_nbd_other0.245
r_nbd_refined0.211
r_symmetry_nbd_other0.21
r_xyhbond_nbd_other0.208
r_xyhbond_nbd_refined0.185
r_nbtor_refined0.169
r_symmetry_nbtor_other0.079
r_chiral_restr0.056
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4687
Nucleic Acid Atoms
Solvent Atoms74
Heterogen Atoms82

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing