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Poly(ADP-ribose) glycohydrolase (PARG) from Drosophila melanogaster in complex with PARG inhibitor PDD00017272
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HMK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 277.15 19% (v/v) PEG3350, 210 mM Na2SO4, 100 mM BisTris propane pH 7.2
Crystal Properties Matthews coefficient Solvent content 3.48 64.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.392 α = 90 b = 115.919 β = 112.205 c = 123.267 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 2018-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.97958 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 2.508 59.02 100 0.122 0.132 0.051 0.996 9.6 6.7 83253
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 2.51 2.58 100 1.829 1.983 0.76 0.511 1.1 6.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6hmk 2.508 59.015 83225 4262 99.789 0.185 0.1826 0.1887 0.2231 0.2292 68.965
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] 0.199 1.02 0.692 -1.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.803 r_dihedral_angle_3_deg 18.163 r_dihedral_angle_6_deg 15.819 r_lrange_it 11.051 r_lrange_other 11.04 r_scangle_it 9.393 r_scangle_other 9.292 r_mcangle_it 8.594 r_mcangle_other 8.593 r_dihedral_angle_1_deg 7.891
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.803 r_dihedral_angle_3_deg 18.163 r_dihedral_angle_6_deg 15.819 r_lrange_it 11.051 r_lrange_other 11.04 r_scangle_it 9.393 r_scangle_other 9.292 r_mcangle_it 8.594 r_mcangle_other 8.593 r_dihedral_angle_1_deg 7.891 r_scbond_it 7.149 r_scbond_other 6.705 r_mcbond_it 6.137 r_mcbond_other 6.131 r_angle_refined_deg 1.681 r_angle_other_deg 0.563 r_symmetry_xyhbond_nbd_refined 0.354 r_symmetry_nbd_refined 0.218 r_nbd_refined 0.204 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.157 r_nbd_other 0.153 r_chiral_restr_other 0.127 r_symmetry_xyhbond_nbd_other 0.088 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.074 r_ncsr_local_group_1 0.064 r_ncsr_local_group_3 0.064 r_ncsr_local_group_2 0.061 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12501 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 168
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing