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Crystal structure of SARS-CoV-2 NSP3 Macrodomain in complex with SRI1.112 at room temperature
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Room temperature apo structure collected not yet deposited
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 292 0.1 M MES (pH 6.50) and 30 % w/v PEG 3000
Crystal Properties Matthews coefficient Solvent content 2.06 40.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.325 α = 90 b = 33.335 β = 97.44 c = 60.893 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 292 PIXEL DECTRIS EIGER2 X 4M 2025-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE VMXi 0.7749 Diamond VMXi
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.53 60.38 100 0.019 1 28.3 148.9 22730
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.53 1.56 100 0.263 0.7 26.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.53 60.38 1.34 22603 1963 99.49 0.156 0.1538 0.1556 0.1782 0.1795
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 11.498 f_angle_d 1.092 f_chiral_restr 0.07 f_bond_d 0.01 f_plane_restr 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1231 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 22
Software Software Software Name Purpose xia2.multiplex data scaling xia2.multiplex data reduction PHASER phasing PHENIX refinement PDB_EXTRACT data extraction