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Human [protein ADP-ribosylargenine] hydrolase ARH1 in complex with ADP-ribose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HFW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 200 mM magnesium formate, 20 % (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.2 44.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.102 α = 90 b = 66.687 β = 90 c = 83.42 γ = 90
Symmetry Space Group P 21 21 21
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 2017-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9760 Diamond I03
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 1.23 66.69 99.6 0.059 0.064 0.025 0.998 21.7 12.2 103868
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 1.23 1.25 97.1 0.262 0.295 0.132 0.981 5.5 9.3
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3HFW 1.23 52.09 98756 5034 99.57 0.14566 0.14506 0.15744 0.1834 RANDOM 19.97
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] 1.02 -0.57 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.93 r_dihedral_angle_4_deg 15.897 r_dihedral_angle_3_deg 13.536 r_dihedral_angle_1_deg 5.305 r_long_range_B_refined 3.083 r_long_range_B_other 2.799 r_angle_refined_deg 1.527 r_scangle_other 1.513 r_angle_other_deg 1.118 r_scbond_it 0.973
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.93 r_dihedral_angle_4_deg 15.897 r_dihedral_angle_3_deg 13.536 r_dihedral_angle_1_deg 5.305 r_long_range_B_refined 3.083 r_long_range_B_other 2.799 r_angle_refined_deg 1.527 r_scangle_other 1.513 r_angle_other_deg 1.118 r_scbond_it 0.973 r_scbond_other 0.971 r_mcangle_other 0.914 r_mcangle_it 0.911 r_mcbond_it 0.573 r_mcbond_other 0.564 r_chiral_restr 0.089 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2794 Nucleic Acid Atoms Solvent Atoms 347 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement xia2 data reduction DIALS data scaling PHASER phasing