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Transglutaminase 3 in complex with inhibitor Z-don and DH patient-derived Fab DH63-A02
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8OXX TG3 in silico model AlphaFold Fab
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 0.15 M phosphate-citrate pH 5.0, 40% ethanol and 5% PEG 400
Crystal Properties Matthews coefficient Solvent content 4.33 71.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.184 α = 90 b = 260.191 β = 95.1 c = 139.024 γ = 90
Symmetry Space Group I 1 2 1
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 EIGER2 X 16M 2023-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.8856 ESRF ID23-1
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 2.9 69.2 99.9 0.122 0.153 0.09 0.983 5.9 5.5 73407
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 2.9 2.96 99.9 1.857 2.345 1.41 0.185 0.6 5.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.9 69.2 73294 3722 99.678 0.197 0.1947 0.2031 0.2425 0.2485 111.633
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] 0.018 2.423 -4.602 4.086
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 23.649 r_lrange_it 23.648 r_mcangle_other 21.251 r_mcangle_it 21.249 r_scangle_it 21.04 r_scangle_other 21.022 r_mcbond_it 15.888 r_mcbond_other 15.877 r_dihedral_angle_3_deg 15.74 r_scbond_it 15.231
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 23.649 r_lrange_it 23.648 r_mcangle_other 21.251 r_mcangle_it 21.249 r_scangle_it 21.04 r_scangle_other 21.022 r_mcbond_it 15.888 r_mcbond_other 15.877 r_dihedral_angle_3_deg 15.74 r_scbond_it 15.231 r_scbond_other 15.217 r_dihedral_angle_6_deg 14.176 r_dihedral_angle_2_deg 14.043 r_dihedral_angle_1_deg 8.733 r_angle_refined_deg 1.012 r_angle_other_deg 0.349 r_symmetry_nbd_other 0.231 r_nbd_refined 0.213 r_nbd_other 0.204 r_symmetry_xyhbond_nbd_refined 0.191 r_nbtor_refined 0.185 r_ncsr_local_group_3 0.173 r_xyhbond_nbd_refined 0.171 r_ncsr_local_group_1 0.17 r_symmetry_nbd_refined 0.169 r_symmetry_nbtor_other 0.084 r_ncsr_local_group_2 0.083 r_chiral_restr 0.054 r_ext_dist_refined_b 0.037 r_symmetry_xyhbond_nbd_other 0.017 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13713 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 131
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing Coot model building