8F02

SARS-CoV-2 Main Protease (Mpro) in Complex with ML2006a4


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5289Sitting drops consisted of 0.23 uL A:0.23 uL B: A) 5.3 mg/mL Mpro + 0.9 mM ML2006a4 in in 20 mM Tris pH 7.3 + 3 mM TCEP + 3 % DMSO B) 0.1 M BICINE pH 8.5, 8% w/v mPEG 5000
Crystal Properties
Matthews coefficientSolvent content
2.2144.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.649α = 90
b = 63.231β = 90
c = 103.798γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MFlat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M22022-10-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.97946SSRLBL12-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
1237.0497.90.1230.0570.9975.54.320441
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
22.1199.62.191.0210.2554.3

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 REPLACEMENTTHROUGHOUT6LZE237.0419391103297.280.192970.189740.25476RANDOM51.68
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]
-0.811.94-1.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.311
r_long_range_B_other9.513
r_long_range_B_refined9.511
r_dihedral_angle_2_deg9.334
r_dihedral_angle_1_deg7.827
r_scangle_other7.369
r_mcangle_other5.741
r_mcangle_it5.74
r_scbond_it4.94
r_scbond_other4.937
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.311
r_long_range_B_other9.513
r_long_range_B_refined9.511
r_dihedral_angle_2_deg9.334
r_dihedral_angle_1_deg7.827
r_scangle_other7.369
r_mcangle_other5.741
r_mcangle_it5.74
r_scbond_it4.94
r_scbond_other4.937
r_mcbond_it4.035
r_mcbond_other4.013
r_angle_refined_deg1.52
r_angle_other_deg0.492
r_chiral_restr0.065
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms2367
Nucleic Acid Atoms
Solvent Atoms49
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
XDSdata reduction
PHASERphasing