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Transglutaminase 3 in complex with DH patient-derived Fab DH63-A02
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8OXX in silico model AlphaFold Fab
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 295 0.15 M phosphate-citrate pH 5.0, 40% ethanol and 5% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.24 45.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.031 α = 90 b = 264.004 β = 106.289 c = 148.7 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 EIGER X 16M 2023-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.9762 MAX IV BioMAX
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 2.8 132.002 99.3 0.176 0.207 0.108 0.994 5.1 7.1 83425
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 2.8 2.86 2.831 3.336 1.747 0.395 7.1
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 2.803 132 83417 4243 99.314 0.207 0.205 0.2082 0.2503 0.2512 107.009
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] -4.769 3.479 -7.571 8.803
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 21.858 r_lrange_other 21.858 r_scangle_it 19.375 r_scangle_other 19.099 r_mcangle_it 18.081 r_mcangle_other 18.08 r_scbond_it 15.04 r_dihedral_angle_3_deg 14.816 r_scbond_other 14.708 r_dihedral_angle_6_deg 14.661
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 21.858 r_lrange_other 21.858 r_scangle_it 19.375 r_scangle_other 19.099 r_mcangle_it 18.081 r_mcangle_other 18.08 r_scbond_it 15.04 r_dihedral_angle_3_deg 14.816 r_scbond_other 14.708 r_dihedral_angle_6_deg 14.661 r_mcbond_it 14.113 r_mcbond_other 14.108 r_dihedral_angle_2_deg 11.746 r_dihedral_angle_1_deg 8.019 r_angle_refined_deg 1.152 r_angle_other_deg 0.389 r_symmetry_xyhbond_nbd_refined 0.324 r_nbd_other 0.288 r_symmetry_nbd_refined 0.242 r_symmetry_nbd_other 0.219 r_nbd_refined 0.207 r_metal_ion_refined 0.185 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.154 r_ncsr_local_group_2 0.136 r_ncsr_local_group_3 0.119 r_symmetry_nbtor_other 0.086 r_symmetry_xyhbond_nbd_other 0.084 r_ncsr_local_group_1 0.083 r_chiral_restr 0.06 r_ext_dist_refined_b 0.055 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13743 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing Coot model building