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Crystal structure of SARS-CoV-2 macrodomain in complex with ADP-ribose-phosphate (ADP-ribose-2'-phosphate, ADPRP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YWK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293.15 30% broad-molecular-weight PEG smears, 0.1 M MgCl2, 0.1 M tris, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.25 45.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.617 α = 90 b = 111.339 β = 90 c = 195.184 γ = 90
Symmetry Space Group P 21 21 21
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 X 16M 2020-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00001 SLS X06SA
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 2.05 48.8 99.7 0.141 0.166 0.064 0.995 8.3 6.2 53878
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 2.05 2.12 99.8 0.839 0.998 0.387 0.695 1.9 6.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6ywk 2.05 48.8 51148 2662 99.47 0.1792 0.1772 0.1862 0.2168 0.2228 RANDOM 26.716
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] 1.04 -0.39 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.092 r_dihedral_angle_4_deg 18.864 r_dihedral_angle_3_deg 12.823 r_dihedral_angle_1_deg 7.396 r_angle_refined_deg 1.426 r_angle_other_deg 1.363 r_chiral_restr 0.072 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.092 r_dihedral_angle_4_deg 18.864 r_dihedral_angle_3_deg 12.823 r_dihedral_angle_1_deg 7.396 r_angle_refined_deg 1.426 r_angle_other_deg 1.363 r_chiral_restr 0.072 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6488 Nucleic Acid Atoms Solvent Atoms 514 Heterogen Atoms 175
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing