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Joint neutron/X-ray structure of SARS-CoV-2 3CL Mpro at room temperature
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6WQF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 287 18% PEG3350, 0.1 M Bis-Tris pH 6.6, 3% DMSO
Crystal Properties Matthews coefficient Solvent content 2.06 40.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.927 α = 90 b = 54.686 β = 101.46 c = 45.216 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 293 PIXEL DECTRIS EIGER R 4M 2020-07-20 M SINGLE WAVELENGTH 2 1 neutron 293 AREA DETECTOR ORNL ANGER CAMERA 2020-07-15 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54 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 2.3 56.32 97.9 0.129 0.07 0.991 9.31 4.3 12094 1 2.5 14.95 83.9 0.19 13 5.7 8031
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 2.3 2.38 0.589 0.355 0.5 1.6 3.7 1 2.5 2.59 0.333 3.7 4.7
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 2.3 28.16 10179 537 82.4 0.185 0.1748 0.22 0.2021 40.27 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 2.5 14.96 8018 413 83.5 0.201 0.253 40.27
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 17.7 x_torsion_deg 17.7 x_angle_deg 1.1 x_angle_deg 1.1 x_torsion_impr_deg 1 x_torsion_impr_deg 1 x_bond_d 0.008 x_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2368 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms
Software Software Software Name Purpose nCNS refinement PHASER phasing CrysalisPro data reduction CrysalisPro data scaling Mantid data reduction Mantid data scaling