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Crystal structure of SARS-CoV-2 (Covid-19) Nsp3 macrodomain in complex with compound 12p
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8GIA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 100 mM Tris-HCl, pH 8, 200 mM sodium acetate, 31% w/v PEG4000
Crystal Properties Matthews coefficient Solvent content 2.24 45.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.91 α = 90 b = 88.9 β = 94.879 c = 43.04 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 S 16M 2024-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE 7B2 0.9686 CHESS 7B2
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 1.526 29.07 95.21 0.08087 0.08792 0.03408 0.998 11.3 6.2 46501 17
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 1.53 1.56 65.94 0.4605 0.5264 0.2452 0.715 1.77 4.1
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 1.53 29.07 1.4 46498 2007 95.21 0.1632 0.1617 0.1627 0.1959 0.1959 20.58
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 18.4909 f_angle_d 0.9862 f_chiral_restr 0.0456 f_bond_d 0.0061 f_plane_restr 0.0042
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2535 Nucleic Acid Atoms Solvent Atoms 309 Heterogen Atoms 128
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing Coot model building