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Human ADP-ribosylhydrolase 3 (ARH3) in complex with ADP
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 15% (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 2.29 46.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.79 α = 116.402 b = 65.76 β = 94.788 c = 69.92 γ = 103.731
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 2024-09-04 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 34.765 96.7 0.105 0.122 0.062 0.995 9.2 3.9 55923 16.2
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 84.3 0.523 0.608 0.309 0.816 2.1 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-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 FREE R-VALUE 1.85 34.765 55923 2000 96.691 0.162 0.162 0.1611 0.172 0.1938 0.2025 Random selection 19.324
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] -0.122 -0.498 -0.405 -0.266 0.307 0.273
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.31 r_dihedral_angle_3_deg 11.584 r_dihedral_angle_2_deg 5.84 r_dihedral_angle_1_deg 5.503 r_lrange_it 4.934 r_lrange_other 4.803 r_scangle_it 3.132 r_scangle_other 3.132 r_mcangle_it 2.203 r_mcangle_other 2.202
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.31 r_dihedral_angle_3_deg 11.584 r_dihedral_angle_2_deg 5.84 r_dihedral_angle_1_deg 5.503 r_lrange_it 4.934 r_lrange_other 4.803 r_scangle_it 3.132 r_scangle_other 3.132 r_mcangle_it 2.203 r_mcangle_other 2.202 r_scbond_it 1.895 r_scbond_other 1.895 r_angle_refined_deg 1.339 r_mcbond_it 1.33 r_mcbond_other 1.33 r_angle_other_deg 0.487 r_symmetry_nbd_refined 0.283 r_nbd_refined 0.218 r_nbtor_refined 0.179 r_symmetry_nbd_other 0.171 r_symmetry_xyhbond_nbd_refined 0.161 r_nbd_other 0.157 r_xyhbond_nbd_refined 0.141 r_symmetry_nbtor_other 0.072 r_chiral_restr 0.071 r_dihedral_angle_other_2_deg 0.008 r_bond_refined_d 0.007 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 5112 Nucleic Acid Atoms Solvent Atoms 537 Heterogen Atoms 73
Software Software Software Name Purpose MxCuBE data collection XDS data reduction XSCALE data scaling PHASER phasing Coot model building REFMAC refinement