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Human ADP-ribosylserine hydrolase ARH3 mutant E41A in complex with ADP-ribose dimer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6D36
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 100 mM TrisHCl (pH 8.5), 20% (w/v) PEG4000 and 200 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.3 46.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.62 α = 90 b = 91.6 β = 105.47 c = 91.09 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 PILATUS3 6M 2019-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96863 Diamond I24
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 1.95 70.631 99.9 0.145 0.083 0.061 0.996 7.9 6.6 99860
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 1.95 2 1.535 1.665 0.638 0.503 1.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6D36 1.95 70.631 99838 4757 99.881 0.188 0.187 0.2106 0.2162 42.84
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] 0.353 0.917 -1.291 0.374
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.943 r_dihedral_angle_4_deg 19.086 r_dihedral_angle_3_deg 13.152 r_dihedral_angle_1_deg 5.718 r_lrange_it 4.741 r_lrange_other 4.74 r_scangle_it 3.197 r_scangle_other 3.197 r_mcangle_it 2.471 r_mcangle_other 2.471
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.943 r_dihedral_angle_4_deg 19.086 r_dihedral_angle_3_deg 13.152 r_dihedral_angle_1_deg 5.718 r_lrange_it 4.741 r_lrange_other 4.74 r_scangle_it 3.197 r_scangle_other 3.197 r_mcangle_it 2.471 r_mcangle_other 2.471 r_scbond_it 1.934 r_scbond_other 1.934 r_mcbond_it 1.515 r_mcbond_other 1.515 r_angle_refined_deg 1.356 r_angle_other_deg 1.347 r_symmetry_xyhbond_nbd_refined 0.332 r_nbd_other 0.201 r_nbd_refined 0.2 r_symmetry_nbd_refined 0.182 r_symmetry_nbd_other 0.17 r_nbtor_refined 0.157 r_xyhbond_nbd_refined 0.149 r_symmetry_nbtor_other 0.079 r_ncsr_local_group_1 0.074 r_chiral_restr 0.071 r_ncsr_local_group_2 0.066 r_ncsr_local_group_6 0.064 r_ncsr_local_group_5 0.063 r_symmetry_xyhbond_nbd_other 0.061 r_ncsr_local_group_3 0.059 r_ncsr_local_group_4 0.058 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 10351 Nucleic Acid Atoms Solvent Atoms 437 Heterogen Atoms 327
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing