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Structure of a catalytically inactive PARG in complex with a poly-ADP-ribose fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EPP PDB ENTRY 4EPP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 0.1 M HEPES, pH 7.0, 30% v/v Jeffamine ED-2001, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.63 53.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.928 α = 90 b = 75.713 β = 90 c = 138.957 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 PILATUS 6M 2012-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.46 29.51 99.6 97166 97166
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 4EPP 1.46 29.51 97166 97166 5111 99.52 0.14031 0.14031 0.13831 0.1474 0.17698 0.1802 RANDOM 13.113
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] 0.31 -0.11 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.443 r_dihedral_angle_4_deg 16.368 r_dihedral_angle_3_deg 11.697 r_scangle_it 7.983 r_dihedral_angle_1_deg 6.102 r_scbond_it 5.569 r_mcangle_it 3.5 r_mcbond_it 2.45 r_rigid_bond_restr 2.338 r_angle_refined_deg 2.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.443 r_dihedral_angle_4_deg 16.368 r_dihedral_angle_3_deg 11.697 r_scangle_it 7.983 r_dihedral_angle_1_deg 6.102 r_scbond_it 5.569 r_mcangle_it 3.5 r_mcbond_it 2.45 r_rigid_bond_restr 2.338 r_angle_refined_deg 2.067 r_angle_other_deg 1.229 r_mcbond_other 0.943 r_chiral_restr 0.152 r_bond_refined_d 0.026 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.002 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3587 Nucleic Acid Atoms Solvent Atoms 462 Heterogen Atoms 62
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XDS data scaling