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Joint X-ray/neutron structure of deuterated SARS-CoV-2 main protease (MPro) in complex with noncovalent inhibitor KB-5
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7N8C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 287 0.1 M HEPES, pH 7.0, 17% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.94 58.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.249 α = 90 b = 81.625 β = 96.6 c = 88.717 γ = 90
Symmetry Space Group I 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 293 PIXEL DECTRIS EIGER R 4M 2026-04-21 M SINGLE WAVELENGTH 2 1 neutron 293 AREA DETECTOR ORNL ANGER CAMERA 2026-04-20 L LAUE 3 1 neutron 293 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5406 2 SPALLATION SOURCE ORNL Spallation Neutron Source BEAMLINE MANDI 2.0-4.0 ORNL Spallation Neutron Source MANDI
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) 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 1.9 30.26 99.9 0.095 0.056 0.979 11 3.9 30828 2 2.3 13.88 91.9 0.179 0.091 0.952 10 3.9 15943
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 0.675 0.379 0.477 1.2 3.9 2 2.3 2.38 0.271 0.132 0.743 4 4
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 1.9 30.26 2.5 26466 1338 85.8 0.2 0.1854 0.215 0.2 random 38.63 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 2.3 13.88 2.5 15469 793 89.2 0.206 0.214 random 38.63
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 x_torsion_deg 30.8 x_angle_deg 1.16 x_torsion_impr_deg 1.01 x_bond_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2368 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 32
Software Software Software Name Purpose nCNS refinement PHASER phasing CrysalisPro data reduction Aimless data scaling Mantid data reduction LAUENORM data scaling