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Joint X-ray/neutron structure of SARS-CoV-2 main protease (3CL Mpro) in complex with BBH-1
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 6.6 287 20% PEG3350, 0.1 M Bis-Tris pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.91 57.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.02 α = 90 b = 81.217 β = 96.72 c = 88.825 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 OSMIC VARIMAX 2021-10-11 M SINGLE WAVELENGTH 2 1 neutron 293 IMAGE PLATE MAATEL COLLIMATORS 2021-10-05 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54 2 NUCLEAR REACTOR ILL BEAMLINE LADI III 3.0-4.0 ILL LADI III
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 1.85 59.75 96.6 0.076 13.6 5.4 32013 2 2.2 44.04 78.7 0.161 0.094 0.986 7.9 3.1 15471
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 1.85 1.92 0.671 1.4 5.4 2 2.2 2.32 0.367 0.223 0.825 2.1 2.9
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 1.85 29.88 33147 28704 1415 86.6 0.197 0.1842 0.21 0.199 33.86 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 2.2 29.9 19760 13060 652 66.1 0.237 0.257 33.86
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 29.4 x_torsion_deg 29.4 x_angle_deg 1.2 x_angle_deg 1.2 x_torsion_impr_deg 0.88 x_torsion_impr_deg 0.88 x_bond_d 0.011 x_bond_d 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2368 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 45
Software Software Software Name Purpose nCNS refinement CrysalisPro data reduction CrysalisPro data scaling PHASER phasing nCNS phasing LAUEGEN data reduction LSCALE data scaling