6Y7M

Crystal structure of the complex resulting from the reaction between the SARS-CoV main protease and tert-butyl (1-((S)-3-cyclohexyl-1-(((S)-4-(cyclopropylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)amino)-1-oxopropan-2-yl)-2-oxo-1,2-dihydropyridin-3-yl)carbamate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62930.1 MES, 6% PEG 6,000, pH 6.0
Crystal Properties
Matthew coefficientSolvent content
3.3763.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.905α = 90
b = 82.247β = 104.465
c = 53.131γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2019-03-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P111.0000PETRA III, DESYP11

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
11.943.6799.40.0480.0560.0280.99812.83.935225
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)
11.9299.10.6390.7420.3720.882.23.8

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2BX41.942.35635112170098.9930.2090.20620.257648.235
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]
-2.7751.7331.7320.132
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.941
r_dihedral_angle_4_deg18.135
r_dihedral_angle_3_deg15.721
r_lrange_it9.061
r_lrange_other9.027
r_dihedral_angle_1_deg7.877
r_scangle_it6.9
r_scangle_other6.898
r_mcangle_other5.865
r_mcangle_it5.865
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.941
r_dihedral_angle_4_deg18.135
r_dihedral_angle_3_deg15.721
r_lrange_it9.061
r_lrange_other9.027
r_dihedral_angle_1_deg7.877
r_scangle_it6.9
r_scangle_other6.898
r_mcangle_other5.865
r_mcangle_it5.865
r_scbond_it4.857
r_scbond_other4.857
r_mcbond_it4.333
r_mcbond_other4.33
r_angle_refined_deg1.822
r_angle_other_deg1.45
r_dihedral_angle_other_3_deg0.321
r_nbd_refined0.214
r_nbd_other0.197
r_xyhbond_nbd_refined0.19
r_symmetry_nbd_other0.189
r_symmetry_xyhbond_nbd_refined0.184
r_chiral_restr0.179
r_nbtor_refined0.176
r_symmetry_nbd_refined0.157
r_symmetry_nbtor_other0.081
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2371
Nucleic Acid Atoms
Solvent Atoms197
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing