6Z2E

Crystal structure of SARS-CoV-2 Mpro in complex with the activity-based probe, biotin-PEG(4)-Abu-Tle-Leu-Gln-vinylsulfone


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6Y2E 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5293.150.12 M Ethylene glycols (0.3 M Diethylene glycol, 0.3 M Triethylene glycol, 0.3 M Tetraethylene glycol, 0.3 M Pentaethylene glycol), 0.1 M buffer system 2 (1.0 M Sodium HEPES, MOPS (acid), pH 7.5), pH 7.5, 30% Precipitant mix 3 (20% glycerol, 10% PEG 4000)
Crystal Properties
Matthews coefficientSolvent content
2.1141.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.083α = 90
b = 104.083β = 90
c = 91.246γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2020-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P111.0332PETRA 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
11.745.621000.0740.0750.012132.438.532640
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)
11.71.791001.5741.5950.2570.86138

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-VALUE6Y2E1.745.24732594162599.9820.1950.1920.243432.48
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]
-0.334-0.167-0.3341.083
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.738
r_dihedral_angle_4_deg15.901
r_dihedral_angle_3_deg13.75
r_dihedral_angle_1_deg7.513
r_lrange_it6.893
r_lrange_other6.828
r_scangle_it5.148
r_scangle_other5.147
r_mcangle_it3.919
r_mcangle_other3.918
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.738
r_dihedral_angle_4_deg15.901
r_dihedral_angle_3_deg13.75
r_dihedral_angle_1_deg7.513
r_lrange_it6.893
r_lrange_other6.828
r_scangle_it5.148
r_scangle_other5.147
r_mcangle_it3.919
r_mcangle_other3.918
r_scbond_it3.548
r_scbond_other3.416
r_mcbond_it2.881
r_mcbond_other2.881
r_angle_refined_deg1.814
r_angle_other_deg1.442
r_dihedral_angle_other_3_deg1.398
r_nbd_refined0.217
r_symmetry_nbd_refined0.204
r_xyhbond_nbd_refined0.202
r_nbd_other0.202
r_symmetry_nbd_other0.189
r_nbtor_refined0.172
r_metal_ion_refined0.13
r_symmetry_xyhbond_nbd_refined0.129
r_chiral_restr0.088
r_symmetry_xyhbond_nbd_other0.088
r_symmetry_nbtor_other0.082
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2368
Nucleic Acid Atoms
Solvent Atoms232
Heterogen Atoms70

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing