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SARS-CoV-2 Mac1 in complex with MCD-628
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8TV6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 298 0.1 M CHES pH 9.5, 32% PEG (w/v) 3000
Crystal Properties Matthews coefficient Solvent content 2.15 42.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.53 α = 90 b = 32.85 β = 94.738 c = 120.6 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2023-05-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.826561 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.1 40.063 100 0.056 1 15.34 6.75 119450
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.1 1.13 100 0.713 1.99 6.72
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.1 40.063 119450 1195 99.948 0.155 0.155 0.1683 0.1748 0.186 17.318
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] -0.38 1.076 -1.306 1.488
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.504 r_dihedral_angle_4_deg 14.987 r_dihedral_angle_3_deg 10.977 r_dihedral_angle_1_deg 6.689 r_lrange_it 3.273 r_lrange_other 3.076 r_scangle_it 2.44 r_scangle_other 2.427 r_rigid_bond_restr 2.265 r_mcangle_it 2.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.504 r_dihedral_angle_4_deg 14.987 r_dihedral_angle_3_deg 10.977 r_dihedral_angle_1_deg 6.689 r_lrange_it 3.273 r_lrange_other 3.076 r_scangle_it 2.44 r_scangle_other 2.427 r_rigid_bond_restr 2.265 r_mcangle_it 2.071 r_mcangle_other 2.071 r_scbond_it 1.848 r_scbond_other 1.845 r_mcbond_it 1.556 r_mcbond_other 1.544 r_angle_other_deg 1.543 r_angle_refined_deg 1.501 r_nbd_refined 0.209 r_symmetry_nbd_refined 0.189 r_nbd_other 0.189 r_symmetry_nbd_other 0.177 r_nbtor_refined 0.169 r_symmetry_xyhbond_nbd_refined 0.152 r_xyhbond_nbd_refined 0.115 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2532 Nucleic Acid Atoms Solvent Atoms 343 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing MxCuBE data collection Coot model building