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Structure of SARS-coV-2 NSP3 macrodomain in complex with ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6WEN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 292 1.8 M K2HPO4/NaH2PO4, pH 8.2
Crystal Properties Matthews coefficient Solvent content 2.24 45.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.8 α = 90 b = 82.8 β = 90 c = 41.27 γ = 120
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 EIGER X 16M 2022-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.977 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.6 41.4 99.99 0.06569 0.06919 0.02159 0.999 24.86 10.3 41759
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.657 0.2766 0.2904 0.08808 0.97 0.2904
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 1.6 41.4 39735 2023 99.99 0.12577 0.12491 0.1624 0.14248 0.1915 RANDOM 23.594
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] 3.5 3.5 -7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.108 r_long_range_B_other 11.526 r_long_range_B_refined 11.485 r_scangle_other 11.215 r_scbond_other 9.29 r_scbond_it 9.262 r_dihedral_angle_1_deg 6.415 r_mcangle_other 6.366 r_mcangle_it 6.348 r_mcbond_it 5.186
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.108 r_long_range_B_other 11.526 r_long_range_B_refined 11.485 r_scangle_other 11.215 r_scbond_other 9.29 r_scbond_it 9.262 r_dihedral_angle_1_deg 6.415 r_mcangle_other 6.366 r_mcangle_it 6.348 r_mcbond_it 5.186 r_mcbond_other 5.14 r_angle_refined_deg 1.177 r_angle_other_deg 0.416 r_chiral_restr 0.053 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2564 Nucleic Acid Atoms Solvent Atoms 366 Heterogen Atoms 60
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHENIX phasing