7O5K
Structure of thaumatin determined at SwissFEL using native-SAD at 6.02 keV with photon energy bandwidth of 2.15% and pinkIndexer with 30000 indexed images
X-RAY DIFFRACTION
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 | 2.05 | 23.14 | 100 | 0.997 | 0.0458 | 12.9 | 356 | 31565 | 43.04 |
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 | 2.05 | 2.1 | 92 | 0.218 | 1.51 | 1.02 |
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 | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | SAD | FREE R-VALUE | 2.05 | 23.14 | 1.34 | 16369 | 818 | 94.81 | 0.1626 | 0.161 | 0.1919 | 44.31 |
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 | 6.515 |
f_angle_d | 0.9955 |
f_chiral_restr | 0.0606 |
f_plane_restr | 0.0118 |
f_bond_d | 0.0086 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1550 |
Nucleic Acid Atoms | |
Solvent Atoms | 78 |
Heterogen Atoms | 10 |
Software
Software | |
---|---|
Software Name | Purpose |
PHENIX | refinement |
CrystFEL | data collection |
CrystFEL | data reduction |
CrystFEL | data scaling |
SHARP | phasing |