8IGN

Crystal structure of SARS-CoV-2 main protease in complex with RAY1216


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7VH8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2890.1 M MES monohydrate pH 6.5, 12% w/v Polyethylene glycol 20,000. Protein concentration 10mg/ml.
Crystal Properties
Matthews coefficientSolvent content
2.8256.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.829α = 80.03
b = 60.935β = 68.34
c = 64.037γ = 70.67
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2022-09-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.97853SSRFBL19U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
1259.4297.50.0679.93.548627
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.050.504

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTFREE R-VALUE2.0257.4745281227597.460.188390.186230.23118RANDOM36.078
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]
3.452.111.04-1.552.610.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.474
r_dihedral_angle_4_deg17.796
r_dihedral_angle_3_deg14.395
r_rigid_bond_restr7.633
r_dihedral_angle_1_deg7.476
r_long_range_B_refined4.882
r_long_range_B_other4.882
r_scangle_other3.528
r_mcangle_other3.213
r_mcangle_it3.204
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.474
r_dihedral_angle_4_deg17.796
r_dihedral_angle_3_deg14.395
r_rigid_bond_restr7.633
r_dihedral_angle_1_deg7.476
r_long_range_B_refined4.882
r_long_range_B_other4.882
r_scangle_other3.528
r_mcangle_other3.213
r_mcangle_it3.204
r_scbond_it2.704
r_scbond_other2.687
r_mcbond_it2.456
r_mcbond_other2.442
r_angle_refined_deg1.479
r_angle_other_deg1.267
r_chiral_restr0.091
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.002
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4642
Nucleic Acid Atoms
Solvent Atoms255
Heterogen Atoms90

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement