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Transglutaminase 3 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 7.1 298 0.1M HEPES-MOPS pH 7.1, 22% ethylene glycol, 11% PEG8000, 10 mM CaCl2, 10 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.82 56.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.505 α = 90 b = 93.488 β = 92.632 c = 90.644 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 EIGER X 4M 2022-05-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
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 1.7 50.02 98.7 0.059 0.083 0.058 0.995 7.1 3 146920
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 1.7 1.73 1.024 1.436 1.005 0.359 2.9
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 1.7 45.315 146656 7468 98.422 0.174 0.1724 0.1658 0.2101 0.2052 33.026
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] -0.43 -0.277 1.752 -1.291
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.52 r_dihedral_angle_3_deg 14.285 r_lrange_it 8.73 r_lrange_other 8.647 r_dihedral_angle_2_deg 8.264 r_dihedral_angle_1_deg 7.61 r_scangle_it 6.192 r_scangle_other 6.191 r_mcangle_it 4.786 r_mcangle_other 4.786
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.52 r_dihedral_angle_3_deg 14.285 r_lrange_it 8.73 r_lrange_other 8.647 r_dihedral_angle_2_deg 8.264 r_dihedral_angle_1_deg 7.61 r_scangle_it 6.192 r_scangle_other 6.191 r_mcangle_it 4.786 r_mcangle_other 4.786 r_scbond_it 4.267 r_scbond_other 4.266 r_mcbond_it 3.382 r_mcbond_other 3.381 r_angle_refined_deg 1.733 r_angle_other_deg 0.594 r_metal_ion_refined 0.274 r_symmetry_nbd_refined 0.255 r_nbd_refined 0.198 r_nbd_other 0.196 r_symmetry_nbd_other 0.195 r_xyhbond_nbd_refined 0.19 r_symmetry_xyhbond_nbd_refined 0.188 r_nbtor_refined 0.179 r_symmetry_xyhbond_nbd_other 0.105 r_symmetry_nbtor_other 0.088 r_chiral_restr 0.085 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 8615 Nucleic Acid Atoms Solvent Atoms 1151 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement Aimless data scaling Coot model building PHASER phasing DIALS data reduction