6Y2E

Crystal structure of the free enzyme of the SARS-CoV-2 (2019-nCoV) main protease


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.1 M MMT (DL-malic acid, MES and Tris base in the molar ratios 1:2:2), pH 7.0, 25% PEG 1,500
Crystal Properties
Matthew coefficientSolvent content
2.0138.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.983α = 90
b = 53.763β = 101.242
c = 44.774γ = 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
11.7548.531000.0820.0890.0340.999156.827173
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.841000.9670.3870.7472.17.1

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2BX41.7548.5327171130999.9710.1740.17120.222425.186
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]
0.636-0.4450.706-1.079
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.02
r_dihedral_angle_3_deg16.155
r_dihedral_angle_4_deg15.211
r_dihedral_angle_1_deg7.865
r_lrange_it6.467
r_lrange_other6.188
r_scangle_it4.371
r_scangle_other4.37
r_scbond_it2.868
r_scbond_other2.866
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.02
r_dihedral_angle_3_deg16.155
r_dihedral_angle_4_deg15.211
r_dihedral_angle_1_deg7.865
r_lrange_it6.467
r_lrange_other6.188
r_scangle_it4.371
r_scangle_other4.37
r_scbond_it2.868
r_scbond_other2.866
r_mcangle_it2.851
r_mcangle_other2.85
r_mcbond_it2.035
r_mcbond_other2.028
r_angle_refined_deg1.566
r_angle_other_deg1.409
r_nbd_other0.219
r_xyhbond_nbd_refined0.211
r_nbd_refined0.204
r_symmetry_xyhbond_nbd_refined0.193
r_symmetry_nbd_refined0.186
r_symmetry_nbd_other0.184
r_nbtor_refined0.17
r_symmetry_nbtor_other0.079
r_chiral_restr0.077
r_gen_planes_refined0.009
r_bond_refined_d0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2367
Nucleic Acid Atoms
Solvent Atoms313
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing