6XHL

Covalent complex of SARS-CoV 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 1UK3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION294Precipitant: 10.0 %w/v (8.0 uL of stock 50.0 %w/v) PEG 6000; Buffer: 0.1 M (4.0 uL of stock 1.0 M) MES (pH 6.00); Additive: 0.0 %v/v (0.0 uL of stock 100.0 %v/v) Dimethyl sulfoxide; Additive: 10.0 % w/v (5.0 uL of stock 80.0 % w/v) Glycerol
Crystal Properties
Matthews coefficientSolvent content
2.3146.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.77α = 90
b = 98.49β = 108.31
c = 59.63γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray98PIXELDECTRIS EIGER X 9M2000-04-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.0APS17-ID

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
11.47156.674.20.0470.0560.030.99912.63.376744
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)
11.4711.5990.5980.7770.4880.5431.5

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 REPLACEMENTTHROUGHOUT1UK31.47156.6176744381474.20.20450.20350.2229RANDOM26.67
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]
-0.37860.33130.06060.318
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion14.82
t_omega_torsion4
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 Atoms4648
Nucleic Acid Atoms
Solvent Atoms375
Heterogen Atoms68

Software

Software
Software NamePurpose
BUSTERrefinement
autoPROCdata scaling
BUSTERphasing
autoPROCdata reduction