8AEB

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, 21% PEG 3350, 10% Glycerol, 8% DMSO
Crystal Properties
Matthews coefficientSolvent content
1.9938.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.141α = 90
b = 53.472β = 101.304
c = 44.65γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2022-06-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 20.980104SOLEILPROXIMA 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
11.8348.37398.70.0930.1110.060.9979.96.223313
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)
11.831.8889.81.221.4640.80.4761.26

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-VALUE7K3T1.8348.37322949117097.110.1860.18350.234131.676
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]
1.2470.718-0.583-0.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.954
r_dihedral_angle_6_deg16.303
r_dihedral_angle_3_deg15.408
r_lrange_it8.806
r_lrange_other8.765
r_dihedral_angle_1_deg8.39
r_scangle_it7.028
r_scangle_other7.026
r_scbond_other5.3
r_scbond_it5.295
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.954
r_dihedral_angle_6_deg16.303
r_dihedral_angle_3_deg15.408
r_lrange_it8.806
r_lrange_other8.765
r_dihedral_angle_1_deg8.39
r_scangle_it7.028
r_scangle_other7.026
r_scbond_other5.3
r_scbond_it5.295
r_mcangle_other4.736
r_mcangle_it4.734
r_mcbond_it3.963
r_mcbond_other3.963
r_angle_refined_deg2.067
r_angle_other_deg0.714
r_metal_ion_refined0.367
r_nbd_refined0.253
r_symmetry_xyhbond_nbd_refined0.249
r_symmetry_nbd_other0.215
r_xyhbond_nbd_refined0.194
r_nbtor_refined0.186
r_symmetry_nbd_refined0.182
r_nbd_other0.172
r_chiral_restr0.099
r_symmetry_nbtor_other0.09
r_bond_refined_d0.014
r_gen_planes_refined0.013
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2341
Nucleic Acid Atoms
Solvent Atoms128
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing