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Joint X-ray/neutron structure of SARS-CoV-2 main protease (Mpro) in complex with Mcule5948770040
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7LTJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 18% PEG3350, 0.1 M Bis-Tris pH 7.0 reservoir solution and 0.2 microL microseeds at 1:200 dilution
Crystal Properties Matthews coefficient Solvent content 2.93 57.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.314 α = 90 b = 81.301 β = 96.46 c = 88.578 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 2021-03-10 M SINGLE WAVELENGTH 2 1 neutron 293 AREA DETECTOR ORNL ANGER CAMERA COLLIMATORS 2021-03-03 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 2.00-4.16 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 2.2 59.72 96.3 0.107 0.055 0.992 11.4 4.7 19108 2 2.5 12.86 85.6 0.212 0.096 0.946 15.6 5.5 11534
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 2.2 2.27 0.602 0.686 1.6 4.8 2 2.5 2.59 0.283 5.8 5.6
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 2.2 25.9 2.5 17476 856 88.1 0.177 0.1682 0.192 0.1895 RANDOM 44.13 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 2.5 12.86 2.5 11532 577 84.9 0.187 0.211 RANDOM 44.13
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 27.1 x_torsion_deg 27.1 x_angle_deg 1.1 x_angle_deg 1.1 x_torsion_impr_deg 0.86 x_torsion_impr_deg 0.86 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 99 Heterogen Atoms 24
Software Software Software Name Purpose nCNS refinement CrysalisPro data reduction CrysalisPro data scaling PHASER phasing nCNS phasing Mantid data reduction LAUENORM data scaling