7UUG

SARS-CoV-2 Main Protease S144A (Mpro S144A) in Complex with ML1006a


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5289.15Sitting drops consisted of 0.19 uL A:0.19 uL B: A) 5.1 mg/mL Mpro S144A + 0.9 mM ML1006a in in 20 mM Tris pH 7.3 + 3 mM TCEP + 3 % DMSO B) 0.1 M MES pH 6.5, 10% PEG20000
Crystal Properties
Matthews coefficientSolvent content
2.2445.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.613α = 90
b = 45.462β = 90
c = 104.749γ = 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 & M22022-03-08MSINGLE 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 Sym I (Observed)Rrim I (All)Rpim I (All)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
12104.74999.90.0610.0670.02613.26.72124221242
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.111001.2691.2691.3740.5210.66.9

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 REPLACEMENTTHROUGHOUT6LZE234.9420152106699.880.18530.18240.2404RANDOM49.11
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]
2.59-1.96-0.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.431
r_dihedral_angle_3_deg15.514
r_dihedral_angle_4_deg14.104
r_dihedral_angle_1_deg7.659
r_angle_refined_deg1.591
r_angle_other_deg1.312
r_chiral_restr0.067
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.431
r_dihedral_angle_3_deg15.514
r_dihedral_angle_4_deg14.104
r_dihedral_angle_1_deg7.659
r_angle_refined_deg1.591
r_angle_other_deg1.312
r_chiral_restr0.067
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2366
Nucleic Acid Atoms
Solvent Atoms68
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction