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Room temperature In-situ SARS-CoV-2 MPRO with bound Z31792168
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 6.5 293 11% (v/v) PEG 4K, 5% (v/v) DMSO, 0.1 M MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.06 40.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.773 α = 90 b = 54.595 β = 101.481 c = 45.313 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 2020-05-19 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 2.26 44.42 98.6 1.7 0.184 0.067 0.994 9.9 7 12834
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 2.26 2.34 99.6 1.956 2.11 0.767 0.425 7
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7AEH 2.26 44.42 12833 646 98.564 0.171 0.1676 0.2313 0.2131 48.917
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] -0.795 -0.947 0.713 0.431
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.284 r_dihedral_angle_3_deg 17.725 r_dihedral_angle_4_deg 14.907 r_dihedral_angle_1_deg 8.351 r_lrange_other 5.197 r_lrange_it 5.166 r_scangle_it 3.408 r_scangle_other 3.407 r_mcangle_it 2.866 r_mcangle_other 2.865
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.284 r_dihedral_angle_3_deg 17.725 r_dihedral_angle_4_deg 14.907 r_dihedral_angle_1_deg 8.351 r_lrange_other 5.197 r_lrange_it 5.166 r_scangle_it 3.408 r_scangle_other 3.407 r_mcangle_it 2.866 r_mcangle_other 2.865 r_scbond_it 2.174 r_scbond_other 2.173 r_mcbond_other 1.847 r_mcbond_it 1.846 r_angle_refined_deg 1.691 r_angle_other_deg 1.314 r_xyhbond_nbd_refined 0.205 r_nbd_refined 0.199 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.17 r_symmetry_xyhbond_nbd_refined 0.167 r_nbd_other 0.163 r_symmetry_nbd_refined 0.155 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.073 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_symmetry_xyhbond_nbd_other 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2325 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing