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Crystal structure of SARS-CoV-2 NSP3 Macrodomain in complex with ASAP-0013775-001
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 40.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.86 α = 90 b = 33.12 β = 96.94 c = 60.43 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 2023-09-07 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 1.47 33.12 99.8 0.094 0.103 0.04 0.998 8.4 6.3 25573
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 1.47 1.51 99.6 1.773 2.008 0.917 0.331 4.6
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 1.47 30.25 25543 1228 99.7 0.2155 0.2138 0.2084 0.2471 0.2345 RANDOM 29.44
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] -2.2208 2.5579 5.9109 -3.6901
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.14 t_omega_torsion 4.23 t_angle_deg 1.12 t_bond_d 0.011 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 1263 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 35
Software Software Software Name Purpose BUSTER refinement Aimless data scaling PHASER phasing XDS data reduction