☰ Navigation Tabs
SARS-CoV-2 Main Protease complexed with N-(pyridin-3-ylmethyl)thioformamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7K3T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2M NaFormate, 21% PEG 3350, 10% Glycerol, 8% DMSO
Crystal Properties Matthews coefficient Solvent content 1.99 38.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.141 α = 90 b = 53.472 β = 101.304 c = 44.65 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 9M 2022-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.980104 SOLEIL PROXIMA 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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.83 48.373 98.7 0.093 0.111 0.06 0.997 9.9 6.2 23313
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) Redundancy Number Unique Reflections (All) 1 1.83 1.88 89.8 1.22 1.464 0.8 0.476 1.2 6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7K3T 1.83 48.373 22949 1170 97.11 0.186 0.1835 0.1822 0.2341 0.234 31.676
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] 1.247 0.718 -0.583 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.954 r_dihedral_angle_6_deg 16.303 r_dihedral_angle_3_deg 15.408 r_lrange_it 8.806 r_lrange_other 8.765 r_dihedral_angle_1_deg 8.39 r_scangle_it 7.028 r_scangle_other 7.026 r_scbond_other 5.3 r_scbond_it 5.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.954 r_dihedral_angle_6_deg 16.303 r_dihedral_angle_3_deg 15.408 r_lrange_it 8.806 r_lrange_other 8.765 r_dihedral_angle_1_deg 8.39 r_scangle_it 7.028 r_scangle_other 7.026 r_scbond_other 5.3 r_scbond_it 5.295 r_mcangle_other 4.736 r_mcangle_it 4.734 r_mcbond_it 3.963 r_mcbond_other 3.963 r_angle_refined_deg 2.067 r_angle_other_deg 0.714 r_metal_ion_refined 0.367 r_nbd_refined 0.253 r_symmetry_xyhbond_nbd_refined 0.249 r_symmetry_nbd_other 0.215 r_xyhbond_nbd_refined 0.194 r_nbtor_refined 0.186 r_symmetry_nbd_refined 0.182 r_nbd_other 0.172 r_chiral_restr 0.099 r_symmetry_nbtor_other 0.09 r_bond_refined_d 0.014 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2341 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing