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Neutron crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at 293 K (C2 crystal form)
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7KQO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 100 mM MES pH 6.5, 25% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.53 51.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.808 α = 90 b = 36.653 β = 98.09 c = 38.233 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 293 PIXEL DECTRIS EIGER R 4M OSMIC VARIMAX 2021-08-30 M SINGLE WAVELENGTH 2 1 neutron 293 AREA DETECTOR ORNL ANGER CAMERA COLLIMATORS 2021-08-30 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54 2 SPALLATION SOURCE ORNL High Flux Isotope Reactor BEAMLINE CG4D 3.3-4.5 ORNL High Flux Isotope Reactor CG4D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) 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 65.74 92.9 0.07 0.036 0.992 19.2 5.6 12576 2 2.3 35.07 75.4 0.151 0.118 0.954 4.4 4 6252
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.02 0.236 0.954 6 5.3 2 2.3 2.4 0.281 0.61 3.2 4.4
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1.95 28.12 12572 608 92.89 0.1322 0.1719 RANDOM 33.44 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 2.3 32.87 6250 330 75.11 0.1873 0.2592 RANDOM 33.44
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 22.5981 f_dihedral_angle_d 22.5981 f_angle_d 1.3541 f_angle_d 1.3541 f_chiral_restr 0.0653 f_chiral_restr 0.0653 f_bond_d 0.0099 f_bond_d 0.0099 f_plane_restr 0.0062 f_plane_restr 0.0062
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1256 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 36
Software Software Software Name Purpose PHENIX refinement Coot model building PHASER phasing