8EZV

SARS-CoV-2 Main Protease (Mpro) in Complex with ML2006a


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8289Sitting drops consisted of 0.23 uL A:0.23 uL B: A) 5.3 mg/mL Mpro + 0.9 mM ML2006a in in 20 mM Tris pH 7.3 + 3 mM TCEP + 3 % DMSO B) 20% v/v 2-Propanol, 0.1 M Tris pH 8.0, 5% w/v PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.2745.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.829α = 90
b = 64.071β = 90
c = 104.422γ = 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 BL12-21.03317SSRLBL12-2

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
11.864.0799.60.1450.1560.0580.99587.229174
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)
11.81.8499.61.8892.0310.7360.6457.2

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 REPLACEMENTTHROUGHOUT6LZE1.854.6727728140199.470.180740.178750.22004RANDOM27.621
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]
-1.440.850.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.064
r_dihedral_angle_2_deg11.906
r_dihedral_angle_1_deg7.174
r_long_range_B_refined6.508
r_long_range_B_other6.407
r_scangle_other4.673
r_mcangle_other3.464
r_mcangle_it3.462
r_scbond_it3.13
r_scbond_other3.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.064
r_dihedral_angle_2_deg11.906
r_dihedral_angle_1_deg7.174
r_long_range_B_refined6.508
r_long_range_B_other6.407
r_scangle_other4.673
r_mcangle_other3.464
r_mcangle_it3.462
r_scbond_it3.13
r_scbond_other3.13
r_mcbond_it2.462
r_mcbond_other2.461
r_angle_refined_deg1.479
r_angle_other_deg0.5
r_chiral_restr0.072
r_gen_planes_refined0.008
r_bond_refined_d0.007
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 Atoms267
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
XDSdata reduction
PHASERphasing