Structure of thaumatin determined at SwissFEL using native-SAD at 6.02 keV with photon energy bandwidth of 2.15% and XGANDALF
Serial Crystallography (SX)
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | BATCH MODE | 7 | 293 | 1.6 M potassium sodium tartrate tetrahydrate, 100 mM Na-HEPES |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.91 | 57.79 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 58.52 | α = 90 |
| b = 58.52 | β = 90 |
| c = 151.3 | γ = 90 |
| Symmetry |
|---|
| Space Group | P 41 21 2 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | x-ray | 297 | PIXEL | PSI JUNGFRAU 16M | | 2019-05-01 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | FREE ELECTRON LASER | SwissFEL ARAMIS BEAMLINE ESA | 2.059 | SwissFEL ARAMIS | ESA |
Serial Crystallography
| Sample delivery method |
|---|
| Diffraction ID | Description | Sample Delivery Method |
|---|
| 1 | | injection |
Data Collection
| Overall |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | CC (Half) | R Split (All) | 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 | 2.2 | 24.8 | 100 | 0.999 | 0.038 | 15.82 | 418 | | 25539 | | | 49.5 |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 2.2 | 2.25 | 100 | | 0.501 | 0.8962 | 1.18 | | |
Refinement
| Statistics |
|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | SAD | FREE R-VALUE | 2.2 | 23.14 | 1.35 | 14057 | 703 | 99.98 | 0.1549 | 0.1528 | 0.15 | 0.1966 | 0.2 | 49.73 |
| 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] |
|---|
| | | | | |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| f_dihedral_angle_d | 13.5984 |
| f_angle_d | 1.1301 |
| f_chiral_restr | 0.0592 |
| f_bond_d | 0.0099 |
| f_plane_restr | 0.0075 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1550 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 46 |
| Heterogen Atoms | 10 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| CrystFEL | data scaling |
| CrystFEL | data reduction |
| SHARP | phasing |
| ARP/wARP | model building |
| PHENIX | refinement |
