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PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of human PARP14 Macrodomain 3 in complex with FMOPL000242a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ABL 4ABL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 277 80 mM KBr, 30 % PEG2kMME
Crystal Properties Matthews coefficient Solvent content 2 38.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.347 α = 90 b = 41.799 β = 90 c = 110.494 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 2017-03-04 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.14 29.17 97.5 0.036 0.04 0.016 0.999 20.5 5 57443
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.14 1.17 76.5 0.495 0.655 0.424 0.723 1.7 3257
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 FOURIER SYNTHESIS THROUGHOUT 4ABL 1.14 55.31 54391 2927 97.28 0.1604 0.1585 0.1684 0.1981 0.199 RANDOM 18.296
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] 0.77 -0.48 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.787 r_sphericity_free 27.132 r_dihedral_angle_4_deg 13.354 r_sphericity_bonded 11.471 r_dihedral_angle_3_deg 11.419 r_dihedral_angle_1_deg 5.809 r_mcangle_it 2.341 r_rigid_bond_restr 2.115 r_mcbond_it 1.915 r_mcbond_other 1.823
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.787 r_sphericity_free 27.132 r_dihedral_angle_4_deg 13.354 r_sphericity_bonded 11.471 r_dihedral_angle_3_deg 11.419 r_dihedral_angle_1_deg 5.809 r_mcangle_it 2.341 r_rigid_bond_restr 2.115 r_mcbond_it 1.915 r_mcbond_other 1.823 r_angle_refined_deg 1.587 r_angle_other_deg 0.981 r_chiral_restr 0.098 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1379 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing