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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 2.29 46.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.501 α = 90 b = 83.501 β = 90 c = 41.426 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 2024-07-23 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 1.95 36.18 99.85 0.1926 0.1978 0.04462 0.998 17.02 19.6 23526
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.02 1.086 1.115 0.869 3.26
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 1.95 36.18 22519 1111 99.85 0.17754 0.17595 0.1849 0.20885 0.2146 RANDOM 25.078
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] 0.42 0.21 0.42 -1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.858 r_long_range_B_other 9.414 r_long_range_B_refined 9.401 r_scangle_other 6.971 r_dihedral_angle_1_deg 5.984 r_mcangle_it 5.168 r_mcangle_other 5.167 r_scbond_other 4.85 r_scbond_it 4.841 r_mcbond_it 3.686
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.858 r_long_range_B_other 9.414 r_long_range_B_refined 9.401 r_scangle_other 6.971 r_dihedral_angle_1_deg 5.984 r_mcangle_it 5.168 r_mcangle_other 5.167 r_scbond_other 4.85 r_scbond_it 4.841 r_mcbond_it 3.686 r_mcbond_other 3.684 r_angle_refined_deg 1.029 r_angle_other_deg 0.385 r_chiral_restr 0.047 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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 334 Heterogen Atoms 60
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction autoPROC data scaling PHASER phasing PDB-REDO refinement