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Human PARP9 2nd macrodomain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3Q71 PDB ENTRY 3Q71
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 30% PEG1000, 0.1M SPG PH 6.0
Crystal Properties Matthews coefficient Solvent content 2.42 49.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.489 α = 90 b = 74.01 β = 90 c = 94.369 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-F 2015-01-26 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 1.55 22.73 97.3 0.09 7.1 4.1 58370
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 1.55 1.58 97.8 0.74 1.7 4.2
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 3Q71 1.55 58.24 55395 2908 96.94 0.17149 0.16921 0.1834 0.21507 0.2209 RANDOM 19.216
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] -0.2 -1.08 1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 41.107 r_dihedral_angle_2_deg 37.239 r_sphericity_free 34.258 r_dihedral_angle_3_deg 11.091 r_sphericity_bonded 9.435 r_dihedral_angle_1_deg 5.733 r_scbond_it 2.766 r_rigid_bond_restr 2.745 r_mcangle_it 2.217 r_mcbond_it 1.753
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 41.107 r_dihedral_angle_2_deg 37.239 r_sphericity_free 34.258 r_dihedral_angle_3_deg 11.091 r_sphericity_bonded 9.435 r_dihedral_angle_1_deg 5.733 r_scbond_it 2.766 r_rigid_bond_restr 2.745 r_mcangle_it 2.217 r_mcbond_it 1.753 r_mcbond_other 1.746 r_angle_refined_deg 1.539 r_angle_other_deg 1.053 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.003 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_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2838 Nucleic Acid Atoms Solvent Atoms 377 Heterogen Atoms 117
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing