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SARS-CoV-2 NSP3 macrodomain in complex with 1-methyl-4-[5-(morpholin-4-ylcarbonyl)-2-furyl]-1H-pyrrolo[2,3-b]pyridine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB
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 2.15 42.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.604 α = 90 b = 88.604 β = 90 c = 39.826 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 2020-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.896844 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 1.95 39.83 100 0.994 5.5 13.4 22915
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 1.95 2 0.603
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 1.95 39.656 22807 1034 99.598 0.182 0.1794 0.1905 0.2262 0.234 27.636
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] -1.966 -1.966 3.932
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.015 r_dihedral_angle_3_deg 13.808 r_dihedral_angle_1_deg 6.977 r_lrange_it 6.246 r_lrange_other 6.22 r_dihedral_angle_2_deg 5.779 r_scangle_it 5.34 r_scangle_other 5.339 r_scbond_it 3.471 r_scbond_other 3.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.015 r_dihedral_angle_3_deg 13.808 r_dihedral_angle_1_deg 6.977 r_lrange_it 6.246 r_lrange_other 6.22 r_dihedral_angle_2_deg 5.779 r_scangle_it 5.34 r_scangle_other 5.339 r_scbond_it 3.471 r_scbond_other 3.47 r_mcangle_other 3.211 r_mcangle_it 3.21 r_mcbond_it 2.293 r_mcbond_other 2.271 r_angle_refined_deg 1.528 r_angle_other_deg 0.504 r_nbd_refined 0.216 r_symmetry_nbd_other 0.19 r_nbd_other 0.184 r_nbtor_refined 0.18 r_symmetry_xyhbond_nbd_refined 0.14 r_xyhbond_nbd_refined 0.125 r_symmetry_nbd_refined 0.09 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.066 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 2526 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing