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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 POB175 (Mac1-x10181)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5S73
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 298 100 mM CHES, pH 9.5, 30% w/v PEG3000
Crystal Properties Matthews coefficient Solvent content 2.14 42.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.55 α = 90 b = 88.55 β = 90 c = 39.615 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 9M 2022-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91788 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 1.22 88.55 87.2 0.041 0.045 0.018 0.998 28.6 5 79818 11.87
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 1.22 1.24 23 0.122 0.172 0.122 0.984 1
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 (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 1.22 88.55 79797 4038 87 0.1464 0.1452 0.1504 0.1691 0.1625 RANDOM 16.76
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] 1.9243 1.9243 -3.8486
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.34 t_omega_torsion 5.63 t_angle_deg 1.21 t_bond_d 0.013 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 14.34 t_omega_torsion 5.63 t_angle_deg 1.21 t_bond_d 0.013 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 2527 Nucleic Acid Atoms Solvent Atoms 452 Heterogen Atoms 38
Software Software Software Name Purpose BUSTER refinement Aimless data scaling XDS data reduction PHASER phasing