8F2D

SARS-CoV-2 Main Protease (Mpro) in Complex with ML4006a


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5289.15Sitting drops consisted of 0.23 uL A:0.23 uL B: A) 5.3 mg/mL Mpro + 0.9 mM ML4006a in in 20 mM Tris pH 7.3 + 3 mM TCEP + 3 % DMSO B) 0.1 M HEPES pH 7.5, 6% PEG 20000
Crystal Properties
Matthews coefficientSolvent content
2.2846.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.396α = 90
b = 64.293β = 90
c = 105.637γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 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)R Merge I (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
11.9537.1197.60.150.1760.0890.9615.5422625
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.95298.51.2761.5010.7740.1524

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 REPLACEMENTTHROUGHOUT6LZE1.9537.1121545105997.120.198820.19620.25211RANDOM26.316
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]
-2.180.81.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.521
r_dihedral_angle_2_deg7.569
r_dihedral_angle_1_deg7.152
r_long_range_B_refined6.505
r_long_range_B_other6.497
r_scangle_other4.825
r_mcangle_other3.498
r_mcangle_it3.48
r_scbond_it3.036
r_scbond_other3.034
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.521
r_dihedral_angle_2_deg7.569
r_dihedral_angle_1_deg7.152
r_long_range_B_refined6.505
r_long_range_B_other6.497
r_scangle_other4.825
r_mcangle_other3.498
r_mcangle_it3.48
r_scbond_it3.036
r_scbond_other3.034
r_mcbond_it2.358
r_mcbond_other2.316
r_angle_refined_deg1.5
r_angle_other_deg0.5
r_chiral_restr0.071
r_bond_refined_d0.008
r_gen_planes_refined0.008
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 Atoms161
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
DIALSdata reduction
PHASERphasing