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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 FMOPL000352a
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 2.01 38.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.28 α = 90 b = 41.67 β = 90 c = 111.24 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 1.05 39.02 85.2 0.04 0.044 0.018 0.998 25.5 4.6 64169
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 15.3 0.201 0.285 0.201 0.88 1.1 849
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 55.68 60805 3287 85.29 0.1365 0.1355 0.1357 0.1566 0.1562 RANDOM 12.816
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] 0.68 -0.11 -0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.936 r_sphericity_free 22.309 r_dihedral_angle_4_deg 19.344 r_dihedral_angle_3_deg 13.223 r_sphericity_bonded 7.951 r_dihedral_angle_1_deg 6.058 r_angle_refined_deg 1.421 r_mcangle_it 1.398 r_rigid_bond_restr 1.125 r_mcbond_it 1.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.936 r_sphericity_free 22.309 r_dihedral_angle_4_deg 19.344 r_dihedral_angle_3_deg 13.223 r_sphericity_bonded 7.951 r_dihedral_angle_1_deg 6.058 r_angle_refined_deg 1.421 r_mcangle_it 1.398 r_rigid_bond_restr 1.125 r_mcbond_it 1.013 r_mcbond_other 1 r_angle_other_deg 0.94 r_chiral_restr 0.089 r_bond_refined_d 0.013 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 209 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing