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Crystal structure of SARS-CoV-2 NSP3 Macrodomain in complex with ASAP-0013388-001
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1 M MES (pH 6.50) and 30 % w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.17 43.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.23 α = 90 b = 33.06 β = 101.34 c = 64.15 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 100 PIXEL DECTRIS EIGER2 XE 9M 2023-07-17 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9212 Diamond I04-1
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 1.15 37.48 70.3 0.09 0.099 0.039 0.995 11 5.5 39392
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 1.15 1.18 7.9 0.855 1.21 0.855 0.487 1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.15 37.48 39375 1993 70.1 0.1633 0.1618 0.1664 0.1922 0.1885 RANDOM 16.76
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] 0.5839 3.3073 1.8784 -2.4623
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.28 t_omega_torsion 5.21 t_angle_deg 1.28 t_bond_d 0.014 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1281 Nucleic Acid Atoms Solvent Atoms 259 Heterogen Atoms 31
Software Software Software Name Purpose BUSTER refinement Aimless data scaling PHASER phasing XDS data reduction