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Crystal structure of SARS-CoV-2 macrodomain in complex with remdesivir metabolite GS-441524
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 8.3 293.15 30% PEG 4000, 0.2 M sodium acetate, 0.1 M tris, pH 8.3
Crystal Properties Matthews coefficient Solvent content 2.07 40.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.238 α = 90 b = 30.476 β = 119.87 c = 111.685 γ = 90
Symmetry Space Group C 1 2 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 X 16M 2020-08-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00003 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 2.15 48.43 99.1 0.09 0.11 0.047 0.998 10.7 5.3 25440
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 2.15 2.23 99.2 0.755 0.912 0.393 0.677 1.9 5.2
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 2.15 48.43 24153 1286 98.81 0.1825 0.1803 0.1902 0.2258 0.2336 RANDOM 48.745
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] 1.23 -0.21 -1.59 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.819 r_dihedral_angle_4_deg 15.149 r_dihedral_angle_3_deg 14.352 r_dihedral_angle_1_deg 7.618 r_angle_refined_deg 1.372 r_angle_other_deg 1.308 r_chiral_restr 0.063 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.819 r_dihedral_angle_4_deg 15.149 r_dihedral_angle_3_deg 14.352 r_dihedral_angle_1_deg 7.618 r_angle_refined_deg 1.372 r_angle_other_deg 1.308 r_chiral_restr 0.063 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3838 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing