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Room temperature In-situ SARS-CoV-2 MPRO with bound Z4439011520
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 2.07 40.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.692 α = 90 b = 54.474 β = 101.698 c = 45.251 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 2020-05-06 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 2.25 44.35 95.2 0.162 0.174 0.061 0.987 8.9 7.2 12607
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 2.25 2.33 1.538 1.652 0.577 0.311 1.1
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 2.25 44.35 12604 618 95.146 0.165 0.1629 0.1633 0.2163 0.2163 47.168
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] 0.392 -0.345 0.252 -0.461
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.119 r_dihedral_angle_4_deg 16.042 r_dihedral_angle_3_deg 15.811 r_dihedral_angle_1_deg 7.883 r_dihedral_angle_other_2_deg 7.052 r_lrange_other 5.127 r_lrange_it 5.126 r_scangle_it 3.428 r_scangle_other 3.427 r_mcangle_it 2.668
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.119 r_dihedral_angle_4_deg 16.042 r_dihedral_angle_3_deg 15.811 r_dihedral_angle_1_deg 7.883 r_dihedral_angle_other_2_deg 7.052 r_lrange_other 5.127 r_lrange_it 5.126 r_scangle_it 3.428 r_scangle_other 3.427 r_mcangle_it 2.668 r_mcangle_other 2.668 r_scbond_it 2.239 r_scbond_other 2.239 r_angle_refined_deg 1.81 r_mcbond_it 1.719 r_mcbond_other 1.716 r_angle_other_deg 1.34 r_symmetry_nbd_refined 0.289 r_chiral_restr 0.284 r_nbd_refined 0.209 r_nbd_other 0.203 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.175 r_symmetry_xyhbond_nbd_refined 0.173 r_xyhbond_nbd_refined 0.154 r_symmetry_nbtor_other 0.085 r_dihedral_angle_other_3_deg 0.032 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2328 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing