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Crystal structure of SARS-CoV-2 NSP3 Macrodomain in complex with SRI1.65 at room temperature
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Room temperature apo structure collected not yet deposited
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 292 0.1 M MES (pH 6.50) and 30 % w/v PEG 3000
Crystal Properties Matthews coefficient Solvent content 2.08 40.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.58 α = 90 b = 33.382 β = 97.94 c = 61.305 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 292 PIXEL DECTRIS EIGER2 X 4M 2024-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE VMXi 0.7749 Diamond VMXi
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.74 60.72 100 0.063 0.997 12.6 39.5 15745
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.74 1.77 100 2.25 0.369 0.8 19.5
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 1.74 60.72 1.33 15610 1476 99.21 0.1587 0.1556 0.1575 0.1881 0.1887
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 5.717 f_angle_d 0.773 f_chiral_restr 0.049 f_bond_d 0.005 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1238 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 12
Software Software Software Name Purpose xia2.multiplex data scaling xia2.multiplex data reduction DIMPLE phasing PHENIX refinement PDB_EXTRACT data extraction