8B2T

SARS-CoV-2 Main Protease (Mpro) in complex with nirmatrelvir alkyne


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6YB7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29311% (v/v) PEG 4K, 5% (v/v) DMSO, 0.1 M MES pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.3146.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.037α = 90
b = 64.392β = 90
c = 104.952γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 X CdTe 2M2022-07-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE VMXm0.58124DiamondVMXm

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.8922.4879.10.5430.5690.1620.9847.616.420055
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.891.947.2227.5192.0550.47522.4

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-VALUE6yb71.89322.481999199578.0290.1840.18240.223430.792
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]
-0.6790.2320.447
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.537
r_dihedral_angle_3_deg13.417
r_lrange_other10.184
r_lrange_it10.18
r_scangle_it8.633
r_scangle_other8.631
r_dihedral_angle_2_deg7.264
r_dihedral_angle_1_deg7.236
r_scbond_it6.502
r_scbond_other6.499
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.537
r_dihedral_angle_3_deg13.417
r_lrange_other10.184
r_lrange_it10.18
r_scangle_it8.633
r_scangle_other8.631
r_dihedral_angle_2_deg7.264
r_dihedral_angle_1_deg7.236
r_scbond_it6.502
r_scbond_other6.499
r_mcangle_other6.301
r_mcangle_it6.291
r_mcbond_it4.633
r_mcbond_other4.62
r_angle_refined_deg1.419
r_angle_other_deg0.472
r_nbd_refined0.206
r_symmetry_nbd_other0.184
r_nbtor_refined0.172
r_xyhbond_nbd_refined0.142
r_symmetry_xyhbond_nbd_refined0.122
r_nbd_other0.114
r_symmetry_nbtor_other0.078
r_chiral_restr0.069
r_symmetry_nbd_refined0.067
r_dihedral_angle_other_1_deg0.007
r_gen_planes_refined0.007
r_bond_refined_d0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2359
Nucleic Acid Atoms
Solvent Atoms83
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
PDB-REDOrefinement
Aimlessdata scaling
xia2.multiplexdata scaling
MOLREPphasing
xia2.multiplexdata reduction