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Group deposition of SARS-CoV-2 NSP3 Macrodomain in complex with inhibitors from the O'Brien group -- Crystal Structure of SARS-CoV-2 NSP3 Macrodomain in complex with POB0206 (Mac1-x10390)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7TX4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 100 mM MES, pH 6.5, 30% w/v PEG4000
Crystal Properties Matthews coefficient Solvent content 2.07 40.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.536 α = 90 b = 33.518 β = 96.68 c = 60.415 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 EIGER2 XE 9M 2023-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92124 Diamond I04-1
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 1.27 59.93 94.2 0.068 0.074 0.03 0.997 7.8 5.3 37415 19.28
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 1.27 1.29 57.6 4.218 5.66 3.723 0.241 2.2
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7TX4 1.295 20 28479 1380 76.1 0.1908 0.1873 0.1912 0.259 0.2425 RANDOM 26.51
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] -2.6574 4.8569 2.7 -0.0425
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.59 t_omega_torsion 4.22 t_angle_deg 1.15 t_bond_d 0.012 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.59 t_omega_torsion 4.22 t_angle_deg 1.15 t_bond_d 0.012 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1256 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms 18
Software Software Software Name Purpose BUSTER refinement Aimless data scaling XDS data reduction PHASER phasing