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Crystal structure of SARS-CoV-2 NSP3 Macrodomain in complex with ASAP-0000453-001
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 2.06 40.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.313 α = 90 b = 33.62 β = 95.96 c = 60.429 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 37.1 76.6 0.042 0.046 0.018 0.996 24.4 5.2 40782
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 1.17 6.7 0.075 0.107 0.075 1 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.15 16.81 40742 1958 76.5 0.1549 0.1528 0.1945 0.1743 RANDOM 21.78
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] -1.6908 4.8369 1.4541 0.2367
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.79 t_omega_torsion 5.42 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 1248 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 28
Software Software Software Name Purpose BUSTER refinement DIALS data scaling DIALS data reduction PHASER phasing