X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 277.15 | Crystals were grown by sitting drop vapor diffusion at 4 degrees C. Drops were set up by mixing 1 uL of protein solution (10 mg/mL in Y sodium phosphate buffer, pH 7.5) with 1 uL of reservoir solution (0.2 M Sodium Fluoride, 20% (w/v) PEG 3350, unbuffered). The drops were incubated for 9 months. The setup was performed using a TTP Labtech Mosquito liquid handling robot. | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.83 | 32.88 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 38.502 | α = 90 |
| b = 61.707 | β = 90 |
| c = 88.128 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 21 |
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 EIGER X 16M | 2024-02-02 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.97625 | Diamond | I03 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 1.13 | 50.55 | 84.1 | 0.057 | 0.06 | 0.99 | 21.8 | 11.1 | 67263 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
| 1 | 1.13 | 1.2 | 11.2 | 0.5 | 0.65 | 0.65 | 1.4 | ||||||||||||
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) | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.13 | 50.55 | 63583 | 3358 | 83.68 | 0.12105 | 0.11981 | 0.12 | 0.14444 | 0.1457 | RANDOM | 8.843 | |||||
| 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] | |
| 1.12 | -1.27 | 0.15 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_long_range_B_refined | 12.902 |
| r_long_range_B_other | 11.298 |
| r_dihedral_angle_3_deg | 11.221 |
| r_dihedral_angle_2_deg | 7.958 |
| r_scangle_other | 6.742 |
| r_dihedral_angle_1_deg | 6.341 |
| r_scbond_it | 4.887 |
| r_scbond_other | 4.885 |
| r_mcangle_other | 4.389 |
| r_mcangle_it | 4.384 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1913 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 277 |
| Heterogen Atoms | 6 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| autoPROC | data scaling |
| autoPROC | data reduction |
| PHASER | phasing |
| PDB_EXTRACT | data extraction |
