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Room temperature In-situ SARS-CoV-2 MPRO with bound Z1367324110
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7AEH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 298 11% (v/v) PEG 4K, 5% (v/v) DMSO, 0.1 M MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.08 40.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.212 α = 90 b = 54.779 β = 101.235 c = 45.336 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 298 PIXEL DECTRIS PILATUS 6M-F 2020-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 1.0 Diamond I24
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 2.11 49.31 99.7 0.17 0.179 0.053 0.996 7.9 9.8 16050
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 2.11 2.19 2.429 2.551 0.755 0.331 1.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7AEH 2.11 44.506 16049 808 99.696 0.179 0.1771 0.1776 0.2221 0.2227 51.605
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] -0.105 -0.357 -0.293 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.974 r_dihedral_angle_4_deg 19.364 r_dihedral_angle_3_deg 15.965 r_dihedral_angle_1_deg 8.189 r_lrange_it 5.77 r_lrange_other 5.761 r_scangle_it 3.716 r_scangle_other 3.715 r_mcangle_other 2.931 r_mcangle_it 2.929
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.974 r_dihedral_angle_4_deg 19.364 r_dihedral_angle_3_deg 15.965 r_dihedral_angle_1_deg 8.189 r_lrange_it 5.77 r_lrange_other 5.761 r_scangle_it 3.716 r_scangle_other 3.715 r_mcangle_other 2.931 r_mcangle_it 2.929 r_scbond_other 2.306 r_scbond_it 2.304 r_angle_refined_deg 1.843 r_mcbond_it 1.831 r_mcbond_other 1.811 r_angle_other_deg 1.384 r_nbd_other 0.293 r_symmetry_nbd_refined 0.226 r_nbd_refined 0.207 r_symmetry_nbd_other 0.203 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.173 r_symmetry_nbtor_other 0.087 r_symmetry_xyhbond_nbd_refined 0.087 r_chiral_restr 0.073 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2324 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing