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Poly(ADP-ribose) glycohydrolase (PARG) from Drosophila melanogaster
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 64.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.433 α = 90 b = 115.622 β = 112.214 c = 122.913 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) 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 2.458 59.025 100 0.11 0.046 0.996 9.7 6.7 88137
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.46 2.52 100 1.618 0.673 0.579 1.2 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 2.474 59.025 85715 4166 99.239 0.18 0.1771 0.1834 0.2277 0.2307 66.609
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] -1.529 -1.236 3.181 -0.482
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.115 r_dihedral_angle_3_deg 19.051 r_dihedral_angle_6_deg 16.647 r_lrange_other 11.867 r_lrange_it 11.864 r_scangle_it 10.288 r_scangle_other 10.062 r_mcangle_other 9.476 r_mcangle_it 9.474 r_scbond_it 8.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.115 r_dihedral_angle_3_deg 19.051 r_dihedral_angle_6_deg 16.647 r_lrange_other 11.867 r_lrange_it 11.864 r_scangle_it 10.288 r_scangle_other 10.062 r_mcangle_other 9.476 r_mcangle_it 9.474 r_scbond_it 8.26 r_dihedral_angle_1_deg 7.813 r_scbond_other 7.565 r_mcbond_it 7.052 r_mcbond_other 7.047 r_angle_refined_deg 1.895 r_angle_other_deg 0.653 r_symmetry_nbd_refined 0.257 r_nbd_refined 0.213 r_symmetry_nbd_other 0.202 r_nbd_other 0.192 r_symmetry_xyhbond_nbd_refined 0.181 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.084 r_ncsr_local_group_3 0.074 r_ncsr_local_group_1 0.073 r_ncsr_local_group_2 0.066 r_bond_refined_d 0.012 r_bond_other_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12552 Nucleic Acid Atoms Solvent Atoms 277 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing