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Transglutaminase 3 in complex with inhibitor Z-don and DH patient-derived Fab DH63-B02
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Other structure in publication
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.1 298 0.1M Hepes-mops pH 7.1, 22% ethylene glycol, 11% PEG8000, 8 mM CaCl2, 8 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.38 48.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.271 α = 90 b = 65.005 β = 96.854 c = 90.908 γ = 90
Symmetry Space Group P 1 21 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 9M 2022-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9184 ESRF ID30B
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 2.5 52.804 94.6 0.1 0.135 0.09 0.994 8.9 3.7 30234
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 2.5 2.6 0.576 0.776 0.516 0.79 3.9
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 2.5 52.804 30222 1532 94.299 0.158 0.1544 0.1544 0.2221 0.2218 43.41
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] 1.347 -1.621 -1.578 0.603
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.129 r_dihedral_angle_3_deg 16.107 r_dihedral_angle_other_3_deg 15.602 r_dihedral_angle_2_deg 13.703 r_lrange_it 9.034 r_lrange_other 9.031 r_dihedral_angle_1_deg 8.196 r_scangle_it 7.432 r_scangle_other 7.431 r_mcangle_other 6.248
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.129 r_dihedral_angle_3_deg 16.107 r_dihedral_angle_other_3_deg 15.602 r_dihedral_angle_2_deg 13.703 r_lrange_it 9.034 r_lrange_other 9.031 r_dihedral_angle_1_deg 8.196 r_scangle_it 7.432 r_scangle_other 7.431 r_mcangle_other 6.248 r_mcangle_it 6.244 r_scbond_it 4.801 r_scbond_other 4.801 r_mcbond_it 4.076 r_mcbond_other 4.072 r_angle_refined_deg 1.652 r_angle_other_deg 0.57 r_symmetry_xyhbond_nbd_refined 0.249 r_nbd_refined 0.209 r_symmetry_nbd_other 0.208 r_nbd_other 0.185 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.169 r_metal_ion_refined 0.152 r_symmetry_nbd_refined 0.121 r_symmetry_nbtor_other 0.088 r_chiral_restr 0.073 r_ext_dist_refined_b 0.014 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6898 Nucleic Acid Atoms Solvent Atoms 453 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Coot model building PHASER phasing XDS data reduction Aimless data scaling