8OXX
Transglutaminase 3 in complex with inhibitor Z-don and DH patient-derived Fab DH63-B02
X-RAY DIFFRACTION
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 | R-Free | Mean Isotropic B | ||||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2.5 | 52.804 | 30222 | 1532 | 94.299 | 0.158 | 0.1544 | 0.2221 | 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 |
| 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 |
