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Crystal structure of SARS-CoV-2 macrodomain in complex with GMP
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 MgCl2, 0.1 M tris, pH 8.3
Crystal Properties Matthews coefficient Solvent content 2.35 47.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.529 α = 90 b = 72.529 β = 90 c = 33.346 γ = 90
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 2020-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00003 SLS X06DA
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 1.55 36.26 99.2 0.064 0.076 0.03 0.998 13.8 6.1 25315
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 1.55 1.6 92.8 0.349 0.455 0.244 0.807 2.6 3.3
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 1.55 36.26 24080 1222 99.08 0.1401 0.1384 0.1514 0.1743 0.1854 RANDOM 16.024
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] 0.14 0.14 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.67 r_dihedral_angle_4_deg 13.095 r_dihedral_angle_3_deg 11.851 r_dihedral_angle_1_deg 6.881 r_angle_refined_deg 1.686 r_angle_other_deg 1.549 r_chiral_restr 0.104 r_bond_refined_d 0.018 r_gen_planes_refined 0.013 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.67 r_dihedral_angle_4_deg 13.095 r_dihedral_angle_3_deg 11.851 r_dihedral_angle_1_deg 6.881 r_angle_refined_deg 1.686 r_angle_other_deg 1.549 r_chiral_restr 0.104 r_bond_refined_d 0.018 r_gen_planes_refined 0.013 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1285 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 84
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing