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Crystal structure of SARS-CoV-2 NSP3 Macrodomain in complex with ASAP-0008351-001
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 293 100 mM CHES (pH 9.5) and 30% PEG-3000
Crystal Properties Matthews coefficient Solvent content 2.17 43.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.25 α = 90 b = 89.25 β = 90 c = 39.6 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 XE 9M 2023-03-02 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 1.26 33.54 96.7 0.096 0.101 0.03 0.998 11.4 7.8 81854
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 1.26 1.29 71.6 1.267 1.659 1.056 0.359 2
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 1.26 18.1 81738 4058 96.7 0.1837 0.1823 0.1798 0.2129 0.2132 RANDOM 22.5
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] 2.0445 2.0445 -4.0889
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.13 t_omega_torsion 4.71 t_angle_deg 1.15 t_bond_d 0.013 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 2519 Nucleic Acid Atoms Solvent Atoms 410 Heterogen Atoms 18
Software Software Software Name Purpose BUSTER refinement Aimless data scaling PHASER phasing XDS data reduction