6Y2F

Crystal structure (monoclinic 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 DROP929310% PEG 200, 0.1 M bis-tris propane, pH 9.0, 18% PEG 8,000
Crystal Properties
Matthew coefficientSolvent content
2.7555.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.085α = 90
b = 80.926β = 114.838
c = 51.659γ = 90
Symmetry
Space GroupC 1 2 1

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
11.9543.3691000.0760.0830.0320.99915.56.826757
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)
11.952.061000.8260.8920.3350.8097

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-VALUE2BX41.9543.36926755129399.9550.180.17790.21914.8336.377
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]
1.854-0.3021.848-2.396
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.242
r_dihedral_angle_4_deg17.946
r_dihedral_angle_3_deg16.049
r_lrange_it8.083
r_lrange_other8.055
r_dihedral_angle_1_deg7.221
r_scangle_it6.008
r_scangle_other6.007
r_mcangle_it4.736
r_mcangle_other4.735
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.242
r_dihedral_angle_4_deg17.946
r_dihedral_angle_3_deg16.049
r_lrange_it8.083
r_lrange_other8.055
r_dihedral_angle_1_deg7.221
r_scangle_it6.008
r_scangle_other6.007
r_mcangle_it4.736
r_mcangle_other4.735
r_scbond_it4.076
r_scbond_other4.075
r_mcbond_other3.252
r_mcbond_it3.251
r_dihedral_angle_other_3_deg1.836
r_angle_refined_deg1.728
r_angle_other_deg1.434
r_nbd_refined0.205
r_symmetry_xyhbond_nbd_refined0.198
r_nbd_other0.18
r_xyhbond_nbd_refined0.18
r_symmetry_nbd_other0.177
r_nbtor_refined0.175
r_symmetry_nbd_refined0.147
r_chiral_restr0.083
r_symmetry_nbtor_other0.08
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2341
Nucleic Acid Atoms
Solvent Atoms177
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing