Thaumatin crystallized in cyclic olefin copolymer-based microfluidic chips
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 1PP3 | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | MICROBATCH | | 277 | 1 M L-sodium potassium tartrate with 0.1 M ADA buffer (pH 6-6.5) |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.93 | 58.04 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 58.666 | α = 90 |
| b = 58.666 | β = 90 |
| c = 151.557 | 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 | 295 | PIXEL | DECTRIS EIGER X 16M | | 2021-12-14 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | SSRL BEAMLINE BL12-1 | 0.979460 | SSRL | BL12-1 |
Serial Crystallography
| Sample delivery method |
|---|
| Diffraction ID | Description | Sample Delivery Method |
|---|
| 1 | | fixed target |
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 | 1.48 | 36.39 | 99.87 | 0.1195 | 0.1259 | 0.03894 | 0.998 | 10.89 | 10.3 | | 45060 | | | 19.67 |
| 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 | 1.48 | 1.533 | 99.95 | | 1.937 | 2.035 | 0.6175 | 0.572 | 0.89 | 10.5 | |
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 (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.48 | 36.39 | 45060 | 2000 | 99.87 | 0.1433 | 0.1426 | 0.14 | 0.1574 | 0.16 | 26.24 |
| 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 | 12.412 |
| f_angle_d | 0.9325 |
| f_chiral_restr | 0.0778 |
| f_plane_restr | 0.0127 |
| f_bond_d | 0.0063 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1552 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 147 |
| Heterogen Atoms | 10 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| xia2 | data reduction |
| xia2 | data scaling |
| PHENIX | phasing |
