6XHM

Covalent complex of SARS-CoV-2 main protease with N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5R8T 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION294Precipitant: 25.0 %w/v (25.0 uL of stock 50.0 %w/v) PEG 1500, Buffer: 0.1 M (5.0 uL of stock 1.0 M) MMT (pH 4.00)
Crystal Properties
Matthews coefficientSolvent content
2.346.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.15α = 90
b = 98.51β = 107.45
c = 59.11γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray98PIXELDECTRIS EIGER X 9M2020-05-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1APS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.40656.39750.0470.99912.33.587382
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.4061.5260.7210.59

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 REPLACEMENTTHROUGHOUT5R8T1.40656.3987382416374.90.19160.19080.2096RANDOM24.33
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]
-0.30190.59820.04140.2604
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion13.96
t_omega_torsion3.94
t_angle_deg0.98
t_bond_d0.008
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4662
Nucleic Acid Atoms
Solvent Atoms445
Heterogen Atoms72

Software

Software
Software NamePurpose
BUSTERrefinement
autoPROCdata scaling
BUSTERphasing
autoPROCdata reduction