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Human poly(ADP-ribose) glycohydrolase in complex with synthetic dimeric ADP-ribose
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 8 20% PEG3350, 0.2 M AMMONIUM SULFATE, 0.1 M PCTP PH 7.5
Crystal Properties Matthews coefficient Solvent content 2.54 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.457 α = 90 b = 91.277 β = 90 c = 96.123 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 2M TORROIDAL MIRROR 2014-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
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 1.95 55.22 99.9 0.1 21.4 13.2 44881
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 1.95 2 99.8 0.58 4.9 12.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4A0D 1.95 66.19 41801 2131 99.88 0.13928 0.1373 0.1789 0.1755 RANDOM 22.196
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] -1.49 -0.27 1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.762 r_dihedral_angle_4_deg 17.86 r_dihedral_angle_3_deg 13.914 r_dihedral_angle_1_deg 6.674 r_scangle_it 5.029 r_scbond_it 3.355 r_mcangle_it 2.944 r_mcbond_it 2.001 r_mcbond_other 1.991 r_angle_refined_deg 1.547
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.762 r_dihedral_angle_4_deg 17.86 r_dihedral_angle_3_deg 13.914 r_dihedral_angle_1_deg 6.674 r_scangle_it 5.029 r_scbond_it 3.355 r_mcangle_it 2.944 r_mcbond_it 2.001 r_mcbond_other 1.991 r_angle_refined_deg 1.547 r_angle_other_deg 1.053 r_chiral_restr 0.106 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 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 4097 Nucleic Acid Atoms Solvent Atoms 422 Heterogen Atoms 197
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing