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SARS-CoV-2 NSP3 macrodomain in complex with aztreonam
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7KQP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 100 mM CHES pH 9.5, 30% PEG3000
Crystal Properties Matthews coefficient Solvent content 2.14 42.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.475 α = 90 b = 88.475 β = 90 c = 39.139 γ = 90
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 EIGER2 XE 16M 2020-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97623 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.9 62.639 95.2 1 62.9 10.8 249288
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 1.9 1.94 0.983
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 7KQP 1.9 62.639 22971 1228 94.839 0.173 0.1705 0.182 0.2141 0.2235 19.547
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] -1.106 -1.106 2.211
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.275 r_dihedral_angle_3_deg 12.631 r_dihedral_angle_1_deg 6.835 r_dihedral_angle_2_deg 5.034 r_lrange_it 5.022 r_lrange_other 5.003 r_scangle_it 3.934 r_scangle_other 3.933 r_mcangle_other 2.606 r_mcangle_it 2.604
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.275 r_dihedral_angle_3_deg 12.631 r_dihedral_angle_1_deg 6.835 r_dihedral_angle_2_deg 5.034 r_lrange_it 5.022 r_lrange_other 5.003 r_scangle_it 3.934 r_scangle_other 3.933 r_mcangle_other 2.606 r_mcangle_it 2.604 r_scbond_it 2.497 r_scbond_other 2.496 r_mcbond_it 1.794 r_mcbond_other 1.794 r_angle_refined_deg 1.623 r_angle_other_deg 0.479 r_nbd_other 0.222 r_nbd_refined 0.219 r_symmetry_xyhbond_nbd_refined 0.215 r_symmetry_nbd_other 0.186 r_symmetry_nbd_refined 0.183 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.119 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.07 r_bond_refined_d 0.008 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 2520 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing