7NTQ

Crystal structure of the SARS-CoV-2 Main Protease complexed with N-(pyridin-3-ylmethyl)thioformamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7K3T 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.2M NaFormate, 20% PEG 3350, 10% Glycerol, 10% DMSO
Crystal Properties
Matthews coefficientSolvent content
1.9737.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.92α = 90
b = 52.91β = 102.88
c = 44.9γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-11-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.978564SOLEILPROXIMA 1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.4947.8498.70.9989.776.942066
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.491.5991.90.51

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-VALUE7K3T1.49543.80942065210498.7120.1730.17060.213223.691
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]
0.473-0.2290.034-0.364
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.03
r_dihedral_angle_4_deg12.973
r_dihedral_angle_3_deg12.37
r_dihedral_angle_1_deg7.279
r_angle_refined_deg1.675
r_angle_other_deg1.458
r_dihedral_angle_other_3_deg0.764
r_symmetry_nbd_refined0.302
r_symmetry_xyhbond_nbd_refined0.278
r_nbd_refined0.233
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.03
r_dihedral_angle_4_deg12.973
r_dihedral_angle_3_deg12.37
r_dihedral_angle_1_deg7.279
r_angle_refined_deg1.675
r_angle_other_deg1.458
r_dihedral_angle_other_3_deg0.764
r_symmetry_nbd_refined0.302
r_symmetry_xyhbond_nbd_refined0.278
r_nbd_refined0.233
r_symmetry_nbd_other0.188
r_nbd_other0.178
r_xyhbond_nbd_refined0.171
r_nbtor_refined0.17
r_chiral_restr0.083
r_symmetry_nbtor_other0.078
r_bond_refined_d0.011
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 Atoms2368
Nucleic Acid Atoms
Solvent Atoms216
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata reduction
Aimlessdata scaling
MOLREPphasing
XDSdata processing