6Y2G

Crystal structure (orthorhombic form) of the complex resulting from the reaction between SARS-CoV-2 (2019-nCoV) main protease and tert-butyl (1-((S)-1-(((S)-4-(benzylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)amino)-3-cyclopropyl-1-oxopropan-2-yl)-2-oxo-1,2-dihydropyridin-3-yl)carbamate (alpha-ketoamide 13b)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52930.1 M Carboxylic acids (0.2 M sodium formate, 0.2 M ammonium acetate, 0.2 M sodium citrate tribasic dihydrate, 0.2 M potassium sodium tartrate tetrahydrate, 0.2 M sodium oxamate), 0.1 M buffer system 3 (1.0 M tris (base), bicine, pH 8.5), pH 8.5, 30% precipitant mix 1 (20% v/v PEG 500 methyl ether, 10% PEG 20,000))
Crystal Properties
Matthew coefficientSolvent content
2.6753.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.566α = 90
b = 101.602β = 90
c = 103.696γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2020-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.9184BESSY14.2

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
12.249.841000.170.1770.0480.99813.113.137519
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.321000.4140.6622.112.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2BX42.241.3937448189899.9470.1890.18620.24735.0740.887
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]
-1.8113.833-2.022
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.937
r_dihedral_angle_4_deg16.509
r_dihedral_angle_3_deg16.48
r_lrange_other9.242
r_lrange_it9.234
r_dihedral_angle_1_deg8.332
r_scangle_it6.786
r_scangle_other6.785
r_mcangle_it5.96
r_mcangle_other5.959
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.937
r_dihedral_angle_4_deg16.509
r_dihedral_angle_3_deg16.48
r_lrange_other9.242
r_lrange_it9.234
r_dihedral_angle_1_deg8.332
r_scangle_it6.786
r_scangle_other6.785
r_mcangle_it5.96
r_mcangle_other5.959
r_dihedral_angle_other_3_deg4.792
r_scbond_it4.528
r_scbond_other4.527
r_mcbond_other4.021
r_mcbond_it4.02
r_angle_refined_deg1.815
r_angle_other_deg1.348
r_nbd_refined0.203
r_symmetry_nbd_other0.185
r_symmetry_xyhbond_nbd_refined0.174
r_nbd_other0.169
r_nbtor_refined0.168
r_xyhbond_nbd_refined0.165
r_symmetry_nbd_refined0.139
r_chiral_restr0.082
r_symmetry_nbtor_other0.079
r_symmetry_xyhbond_nbd_other0.058
r_xyhbond_nbd_other0.035
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4669
Nucleic Acid Atoms
Solvent Atoms313
Heterogen Atoms90

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing