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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 POB0213 (Mac1-x10581)
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 2.05 39.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.137 α = 90 b = 33.645 β = 95.75 c = 60.243 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 2025-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92204 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 1.15 36.94 72.7 0.038 0.041 0.016 0.998 25.3 5.4 38405
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.15 1.17 5.6 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 (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 1.15 12.94 38212 1863 72.3 0.1707 0.1686 0.1743 0.2104 0.201 RANDOM 26.83
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] -2.9594 3.9146 3.5847 -0.6253
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.91 t_omega_torsion 5.02 t_angle_deg 1.22 t_bond_d 0.014 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.91 t_omega_torsion 5.02 t_angle_deg 1.22 t_bond_d 0.014 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion 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 183 Heterogen Atoms 26
Software Software Software Name Purpose BUSTER refinement Aimless data scaling XDS data reduction PHASER phasing