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Crystal structure of SARS-CoV-2 3CL protease in complex with inhibitor NN-IV-105
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XMK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 291 15% (w/v) PEG 1500, 100 mM SPG pH 9.0
Crystal Properties Matthews coefficient Solvent content 2.21 44.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.858 α = 90 b = 98.372 β = 107.65 c = 58.664 γ = 90
Symmetry Space Group P 1 21 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 EIGER2 XE 9M 2023-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.97956 NSLS-II 19-ID
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 1.65 48.6 97.2 0.047 0.05 0.019 1 17.2 7.1 69168
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 1.65 1.68 95.4 1.089 1.172 0.429 0.847 7.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.65 48.6 1.34 68935 3473 96.78 0.185 0.1835 0.1853 0.212 0.2101
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.813 f_angle_d 1.012 f_chiral_restr 0.057 f_plane_restr 0.011 f_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4575 Nucleic Acid Atoms Solvent Atoms 263 Heterogen Atoms 102
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction