☰ Navigation Tabs
Transglutaminase 3 zymogen in complex with DH patient-derived Fab DH63-B02
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NUG in silico model AlphaFold Fab
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.1 298 0.1M HEPES-MOPS pH7.1, 15% ethylene glycol, 7.5% PEG8000, 6 mM CaCl2, 6 mM MgCl2. 20% Ethylene glycol in the cryo solution.
Crystal Properties Matthews coefficient Solvent content 2.85 56.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.659 α = 90 b = 94.04 β = 93.463 c = 91.143 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 PILATUS3 2M 2022-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8731 ESRF ID23-2
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 1.8 41.806 99.9 0.096 0.122 0.074 0.987 6.7 4.5 127215
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 1.8 1.83 1.167 1.513 0.952 0.457 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 1.8 41.806 127154 6326 99.91 0.188 0.1854 0.1839 0.229 0.2304 33.842
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] -0.155 -0.527 0.379 -0.159
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.098 r_dihedral_angle_3_deg 14.769 r_dihedral_angle_2_deg 9.942 r_lrange_it 8.829 r_lrange_other 8.725 r_dihedral_angle_1_deg 7.774 r_scangle_it 5.48 r_scangle_other 5.479 r_mcangle_it 4.645 r_mcangle_other 4.645
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.098 r_dihedral_angle_3_deg 14.769 r_dihedral_angle_2_deg 9.942 r_lrange_it 8.829 r_lrange_other 8.725 r_dihedral_angle_1_deg 7.774 r_scangle_it 5.48 r_scangle_other 5.479 r_mcangle_it 4.645 r_mcangle_other 4.645 r_scbond_it 3.64 r_scbond_other 3.64 r_mcbond_it 3.135 r_mcbond_other 3.135 r_angle_refined_deg 1.712 r_angle_other_deg 0.578 r_xyhbond_nbd_refined 0.21 r_nbd_refined 0.201 r_symmetry_nbd_other 0.199 r_symmetry_xyhbond_nbd_refined 0.186 r_metal_ion_refined 0.181 r_nbtor_refined 0.18 r_symmetry_nbd_refined 0.173 r_nbd_other 0.161 r_symmetry_nbtor_other 0.088 r_chiral_restr 0.083 r_symmetry_xyhbond_nbd_other 0.016 r_bond_refined_d 0.011 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 8632 Nucleic Acid Atoms Solvent Atoms 1346 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction PHASER phasing Coot model building BUCCANEER model building