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Human [protein ADP-ribosylargenine] hydrolase ARH1 in complex with ADP-HPM
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, HANGING DROP 7.5 293.15 100 mM magnesium acetate, 12 % (w/v) PEG8000, 100 mM MOPS pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.04 39.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.526 α = 90 b = 42.94 β = 118.93 c = 89.231 γ = 90
Symmetry Space Group C 1 2 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 PILATUS 6M-F 2018-01-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 1.0036 Diamond I04
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 1.8 78.09 99.4 0.07 0.083 0.044 0.999 12.8 6.4 30388
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 1.8 1.84 99.5 0.488 0.575 0.302 0.886 2.7 5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3HFW 1.8 78.09 28819 1569 99.39 0.18351 0.18143 0.1897 0.22039 0.2248 RANDOM 30.432
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] -1.28 -1.02 2.16 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.265 r_dihedral_angle_3_deg 15.507 r_dihedral_angle_4_deg 15.443 r_dihedral_angle_1_deg 6.063 r_long_range_B_refined 2.28 r_long_range_B_other 2.247 r_angle_refined_deg 1.455 r_scangle_other 1.257 r_angle_other_deg 1.031 r_mcangle_it 0.931
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.265 r_dihedral_angle_3_deg 15.507 r_dihedral_angle_4_deg 15.443 r_dihedral_angle_1_deg 6.063 r_long_range_B_refined 2.28 r_long_range_B_other 2.247 r_angle_refined_deg 1.455 r_scangle_other 1.257 r_angle_other_deg 1.031 r_mcangle_it 0.931 r_mcangle_other 0.931 r_scbond_it 0.8 r_scbond_other 0.8 r_mcbond_it 0.594 r_mcbond_other 0.589 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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 2814 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement xia2 data reduction DIALS data scaling PHASER phasing