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Structure of human PARG catalytic domain in complex with ADP-HPD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4A0D PDB ENTRY 4A0D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 25% PEG 3350, 36.4 MM PCTP-4, 63.6 MM PCTP-10, 0.2 M AMMONIUM SULPHATE
Crystal Properties Matthews coefficient Solvent content 2.47 50.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.848 α = 90 b = 90.971 β = 90 c = 94.763 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 CCD RIGAKU SATURN 944 VARIMAXHF 2010-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.08 94.76 90.2 0.11 12.4 6.3 32176 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.08 2.19 52.7 0.49 2.8 3.7
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 (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 4A0D 2.08 65.63 30387 1601 90.37 0.17018 0.1678 0.1743 0.21475 0.2226 RANDOM 24.065
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] -2.01 -0.23 2.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.158 r_dihedral_angle_4_deg 15.777 r_dihedral_angle_3_deg 15.122 r_dihedral_angle_1_deg 6.087 r_scangle_it 3.033 r_scbond_it 1.915 r_angle_refined_deg 1.416 r_mcangle_it 1.298 r_angle_other_deg 1.103 r_mcbond_it 0.718
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.158 r_dihedral_angle_4_deg 15.777 r_dihedral_angle_3_deg 15.122 r_dihedral_angle_1_deg 6.087 r_scangle_it 3.033 r_scbond_it 1.915 r_angle_refined_deg 1.416 r_mcangle_it 1.298 r_angle_other_deg 1.103 r_mcbond_it 0.718 r_mcbond_other 0.164 r_chiral_restr 0.09 r_bond_refined_d 0.014 r_bond_other_d 0.006 r_gen_planes_refined 0.006 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4060 Nucleic Acid Atoms Solvent Atoms 529 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling AMoRE phasing