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Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z9941018035
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7KQO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 293 100 mM CHES, 32% PEG 3000
Crystal Properties Matthews coefficient Solvent content 2.15 42.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.584 α = 90 b = 88.584 β = 90 c = 39.593 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 S 16M 2026-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.8856 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 0.97 44.29 83.5 0.051 0.02 0.999 15.7 6 151548 10.98
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.97 0.99 14.7 1.442 0.975 0.344 0.6 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 0.97 39.62 1.35 151470 7564 83.46 0.1307 0.1298 0.1289 0.1491 0.1479 16.67
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.9981 f_angle_d 1.0674 f_chiral_restr 0.0773 f_plane_restr 0.0126 f_bond_d 0.0084
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2535 Nucleic Acid Atoms Solvent Atoms 504 Heterogen Atoms 49
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing