Crystal structure of human Signal Regulatory Protein 2 (SIRP) alpha V2 in complex with 5-Hydroxy-L-Tryptophan
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2JJS | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 293 | 0.01M Zinc sulfate heptahydrate 0.1M MES monohydrate pH 6.5 25% v/v PEG monomethyl ether 550 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.11 | 41.7 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 57.457 | α = 90 |
| b = 57.457 | β = 90 |
| c = 198.156 | 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 | 100 | PIXEL | DECTRIS EIGER X 16M | 2020-09-03 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SOLEIL BEAMLINE PROXIMA 1 | 0.978565 | SOLEIL | PROXIMA 1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.5 | 49.7 | 100 | 0.108 | 1 | 19.23 | 25 | 54272 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 1 | 1.5 | 1.59 | 1.167 | 0.666 | |||||||||||||||
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 | 1.5 | 49.54 | 51557 | 2714 | 99.98 | 0.23279 | 0.23172 | 0.2387 | 0.25306 | 0.264 | RANDOM | 24.625 | |||||
| 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] | |
| -0.46 | -0.46 | 0.91 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_3_deg | 12.819 |
| r_dihedral_angle_1_deg | 6.975 |
| r_dihedral_angle_2_deg | 6.067 |
| r_long_range_B_refined | 5.579 |
| r_long_range_B_other | 5.554 |
| r_scangle_other | 4.103 |
| r_mcangle_it | 3.091 |
| r_mcangle_other | 3.091 |
| r_scbond_it | 2.687 |
| r_scbond_other | 2.685 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2594 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 206 |
| Heterogen Atoms | 22 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data scaling |
| XDS | data reduction |
| PHASER | phasing |
| PDB_EXTRACT | data extraction |
