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Human ADP-ribosylhydrolase 3 (ARH3) in complex with an inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FOZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 277 10% (w/v) PEG 4000, 10% (v/v) DMSO, 0.1 M ammonium sulfate, 0.1 M sodium acetate buffer
Crystal Properties Matthews coefficient Solvent content 2.35 47.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.22 α = 115.28 b = 66.02 β = 96.392 c = 70.86 γ = 104.332
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 EIGER X 4M 2024-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
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 1.85 35.995 96.6 0.056 0.065 0.033 0.998 14.4 3.9 57348 24.1
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 1.85 1.898 84.7 0.433 0.504 0.257 0.869 2.8 3.8
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.85 35.995 57348 2000 96.58 0.164 0.1627 0.1724 0.2029 0.2116 Random selection 34.951
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] -0.36 -0.544 -0.808 -0.481 0.909 0.267
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.041 r_dihedral_angle_2_deg 11.956 r_dihedral_angle_3_deg 11.899 r_lrange_it 5.549 r_lrange_other 5.508 r_dihedral_angle_1_deg 5.269 r_scangle_it 3.357 r_scangle_other 3.356 r_dihedral_angle_other_2_deg 3.154 r_mcangle_it 2.143
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.041 r_dihedral_angle_2_deg 11.956 r_dihedral_angle_3_deg 11.899 r_lrange_it 5.549 r_lrange_other 5.508 r_dihedral_angle_1_deg 5.269 r_scangle_it 3.357 r_scangle_other 3.356 r_dihedral_angle_other_2_deg 3.154 r_mcangle_it 2.143 r_mcangle_other 2.143 r_scbond_it 2.068 r_scbond_other 2.067 r_mcbond_it 1.4 r_mcbond_other 1.381 r_angle_refined_deg 1.357 r_angle_other_deg 0.498 r_symmetry_nbd_refined 0.287 r_nbd_refined 0.22 r_nbtor_refined 0.18 r_symmetry_nbd_other 0.173 r_nbd_other 0.148 r_xyhbond_nbd_refined 0.138 r_symmetry_xyhbond_nbd_refined 0.124 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5051 Nucleic Acid Atoms Solvent Atoms 340 Heterogen Atoms 48
Software Software Software Name Purpose MxCuBE data collection XDS data reduction XSCALE data scaling PHASER phasing Coot model building REFMAC refinement