8EYJ

Crystal Structure of uncleaved SARS-CoV-2 Main Protease C145S 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% DMSO, 8% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.6353.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.646α = 90
b = 101.969β = 90
c = 103.626γ = 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)R Merge I (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
11.738101.96971.50.070.9958.96.753189
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)
11.7381.80.4760.5561.4

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-VALUE7MBG1.73872.78853188259471.50.1950.19310.233925.399
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]
-0.0090.172-0.163
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.243
r_dihedral_angle_4_deg17.571
r_dihedral_angle_3_deg13.138
r_lrange_it7.473
r_dihedral_angle_1_deg7.29
r_lrange_other7.071
r_scangle_it4.13
r_scangle_other4.129
r_mcangle_other3.367
r_mcangle_it3.366
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.243
r_dihedral_angle_4_deg17.571
r_dihedral_angle_3_deg13.138
r_lrange_it7.473
r_dihedral_angle_1_deg7.29
r_lrange_other7.071
r_scangle_it4.13
r_scangle_other4.129
r_mcangle_other3.367
r_mcangle_it3.366
r_scbond_it2.603
r_scbond_other2.603
r_mcbond_other2.11
r_mcbond_it2.109
r_angle_refined_deg1.487
r_angle_other_deg1.423
r_symmetry_xyhbond_nbd_refined0.285
r_xyhbond_nbd_refined0.228
r_nbd_other0.216
r_nbd_refined0.204
r_symmetry_nbd_other0.199
r_symmetry_nbd_refined0.197
r_nbtor_refined0.169
r_symmetry_nbtor_other0.081
r_symmetry_xyhbond_nbd_other0.075
r_chiral_restr0.073
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4684
Nucleic Acid Atoms
Solvent Atoms713
Heterogen Atoms70

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing