8E25

Crystal Structure of SARS-CoV-2 Main Protease M49I 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 DIFFUSION, SITTING DROP2930.1 M MES pH 6.7, 5% DMSO, 8% PEG 4000 Cryo protected with 40% PEG 400
Crystal Properties
Matthews coefficientSolvent content
2.652.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.859α = 90
b = 100.068β = 90
c = 103.533γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2022-05-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS SIRIUS BEAMLINE MANACA0.977180LNLS SIRIUSMANACA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.86872.05651.420.0840.9897.45.630317
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.8681.9372.370.3770.6841.6

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-VALUE7MBG1.86872.05630317149351.2460.1960.1940.2433.494
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]
0.2060.119-0.325
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.833
r_dihedral_angle_3_deg16.561
r_dihedral_angle_4_deg16.488
r_dihedral_angle_1_deg7.838
r_lrange_it6.779
r_lrange_other6.749
r_scangle_it4.348
r_scangle_other4.348
r_mcangle_it3.735
r_mcangle_other3.734
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.833
r_dihedral_angle_3_deg16.561
r_dihedral_angle_4_deg16.488
r_dihedral_angle_1_deg7.838
r_lrange_it6.779
r_lrange_other6.749
r_scangle_it4.348
r_scangle_other4.348
r_mcangle_it3.735
r_mcangle_other3.734
r_scbond_it2.66
r_scbond_other2.66
r_mcbond_it2.289
r_mcbond_other2.288
r_angle_refined_deg1.454
r_angle_other_deg1.274
r_symmetry_xyhbond_nbd_refined0.28
r_nbd_other0.234
r_xyhbond_nbd_refined0.214
r_nbd_refined0.193
r_symmetry_nbd_other0.192
r_symmetry_nbd_refined0.168
r_nbtor_refined0.164
r_symmetry_nbtor_other0.081
r_chiral_restr0.062
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 Atoms4680
Nucleic Acid Atoms
Solvent Atoms202
Heterogen Atoms82

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing