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Transglutaminase 3 without calcium in complex with DH patient-derived Fab DH63-B02
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Other structure in paper
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 0.1 M Bicine-Tris pH 8.5, 22% Ethylene glycol, 11% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.72 54.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.022 α = 90 b = 92.275 β = 92.31 c = 90.359 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 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 60.43 99.9 0.112 0.151 0.1 0.992 5.5 3.7 88598
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 2.04 0.92 1.231 0.812 0.599 3.7
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 58.765 88561 4529 99.873 0.178 0.1758 0.1745 0.2261 0.2263 33.537
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] -1.572 -0.236 1.435 0.155
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.192 r_dihedral_angle_3_deg 15.041 r_dihedral_angle_2_deg 8.678 r_lrange_it 8.588 r_lrange_other 8.491 r_dihedral_angle_1_deg 7.899 r_scangle_it 6.119 r_scangle_other 6.108 r_mcangle_it 4.383 r_mcangle_other 4.383
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.192 r_dihedral_angle_3_deg 15.041 r_dihedral_angle_2_deg 8.678 r_lrange_it 8.588 r_lrange_other 8.491 r_dihedral_angle_1_deg 7.899 r_scangle_it 6.119 r_scangle_other 6.108 r_mcangle_it 4.383 r_mcangle_other 4.383 r_scbond_it 4.083 r_scbond_other 3.958 r_mcbond_it 2.886 r_mcbond_other 2.886 r_angle_refined_deg 1.663 r_angle_other_deg 0.563 r_symmetry_xyhbond_nbd_refined 0.231 r_xyhbond_nbd_refined 0.224 r_nbd_other 0.216 r_nbd_refined 0.205 r_symmetry_nbd_other 0.202 r_nbtor_refined 0.183 r_symmetry_nbd_refined 0.179 r_symmetry_xyhbond_nbd_other 0.11 r_symmetry_nbtor_other 0.09 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8600 Nucleic Acid Atoms Solvent Atoms 829 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing Coot model building DIALS data reduction