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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 FMSOA000341b
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 1.99 38.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.32 α = 90 b = 41.48 β = 90 c = 110.73 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 2017-02-10 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 1.05 55.37 82.8 0.035 0.038 0.016 0.999 20.8 4.8 61811
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 1.05 1.08 14.3 0.334 0.462 0.316 0.697 1.1 772
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 1.05 55.43 58583 3149 82.78 0.1427 0.1416 0.1429 0.1656 0.1655 RANDOM 14.12
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] 0.73 -0.31 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.279 r_sphericity_free 27.9 r_dihedral_angle_4_deg 22.564 r_dihedral_angle_3_deg 11.671 r_sphericity_bonded 7.524 r_dihedral_angle_1_deg 5.654 r_angle_refined_deg 1.515 r_mcangle_it 1.479 r_rigid_bond_restr 1.333 r_mcbond_it 1.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.279 r_sphericity_free 27.9 r_dihedral_angle_4_deg 22.564 r_dihedral_angle_3_deg 11.671 r_sphericity_bonded 7.524 r_dihedral_angle_1_deg 5.654 r_angle_refined_deg 1.515 r_mcangle_it 1.479 r_rigid_bond_restr 1.333 r_mcbond_it 1.085 r_mcbond_other 1.079 r_angle_other_deg 1.003 r_chiral_restr 0.098 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1380 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing