7ZQV

Structure of the SARS-CoV-2 main protease in complex with AG7404


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6Y2E 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293Sodium chloride, HEPES pH 7 and PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.0640.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.309α = 90
b = 54.082β = 100.34
c = 115.011γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2021-07-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.96770ESRFBM30A

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
12.2648.8489.50.9854.52.518801
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)
12.262.450.802

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 REPLACEMENTTHROUGHOUT6y2e2.2648.841792887372.670.192520.19020.24054RANDOM40.67
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]
0.09-0.11-0.390.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.101
r_dihedral_angle_4_deg19.643
r_dihedral_angle_3_deg17.954
r_dihedral_angle_1_deg7.98
r_long_range_B_refined7.791
r_long_range_B_other7.79
r_scangle_other5.186
r_mcangle_it4.505
r_mcangle_other4.505
r_scbond_it3.214
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.101
r_dihedral_angle_4_deg19.643
r_dihedral_angle_3_deg17.954
r_dihedral_angle_1_deg7.98
r_long_range_B_refined7.791
r_long_range_B_other7.79
r_scangle_other5.186
r_mcangle_it4.505
r_mcangle_other4.505
r_scbond_it3.214
r_scbond_other3.214
r_mcbond_it2.815
r_mcbond_other2.814
r_angle_refined_deg1.444
r_angle_other_deg1.194
r_chiral_restr0.058
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4716
Nucleic Acid Atoms
Solvent Atoms104
Heterogen Atoms76

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing