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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 FMOPL000462a
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 38.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.341 α = 90 b = 41.653 β = 90 c = 111.018 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 1.17 29.2 99 0.043 0.047 0.019 0.999 16.5 5.2 54380
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 1.17 1.2 88.2 0.481 0.611 0.37 0.842 2.2 3529
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 FOURIER SYNTHESIS THROUGHOUT 4ABL 1.17 55.57 51501 2781 98.85 0.1517 0.15 0.1863 0.1939 RANDOM 19.117
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] 1.32 -0.31 -1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.255 r_sphericity_free 26.327 r_dihedral_angle_4_deg 16.684 r_dihedral_angle_3_deg 12.389 r_sphericity_bonded 10.247 r_dihedral_angle_1_deg 5.69 r_mcangle_it 2.103 r_rigid_bond_restr 1.968 r_mcbond_it 1.596 r_angle_refined_deg 1.595
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.255 r_sphericity_free 26.327 r_dihedral_angle_4_deg 16.684 r_dihedral_angle_3_deg 12.389 r_sphericity_bonded 10.247 r_dihedral_angle_1_deg 5.69 r_mcangle_it 2.103 r_rigid_bond_restr 1.968 r_mcbond_it 1.596 r_angle_refined_deg 1.595 r_mcbond_other 1.585 r_angle_other_deg 0.997 r_chiral_restr 0.101 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1380 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing