7YGG
Crystal structure of human CD47 in complex with engineered SIRPa.D1(N80A)
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | APS BEAMLINE 19-ID |
| Synchrotron site | APS |
| Beamline | 19-ID |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2022-04-02 |
| Detector | DECTRIS PILATUS3 X 6M |
| Wavelength(s) | 0.97935 |
| Spacegroup name | P 21 21 21 |
| Unit cell lengths | 53.580, 99.640, 138.930 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 47.190 - 2.760 |
| R-factor | 0.2196 |
| Rwork | 0.217 |
| R-free | 0.26480 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 5tz2 2jjs |
| RMSD bond length | 0.003 |
| RMSD bond angle | 1.214 |
| Data reduction software | XDS (1.10.2022) |
| Data scaling software | Aimless (0.7.7) |
| Phasing software | PHASER (2.8.3) |
| Refinement software | REFMAC (5.8.0267) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 47.190 | 47.190 | 2.910 |
| High resolution limit [Å] | 2.760 | 8.730 | 2.760 |
| Rmerge | 0.288 | 0.069 | 1.419 |
| Rmeas | 0.309 | 0.074 | 1.523 |
| Rpim | 0.109 | 0.027 | 0.542 |
| Total number of observations | 168759 | 5691 | 23082 |
| Number of reflections | 19839 | 720 | 2810 |
| <I/σ(I)> | 10.1 | 24.5 | 2.6 |
| Completeness [%] | 100.0 | 99.6 | 99.9 |
| Redundancy | 8.5 | 7.9 | 8.2 |
| CC(1/2) | 0.977 | 0.997 | 0.517 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 291 | 0.2M Lithium sulfate, 0.1M Tris pH 8.5, 30% w/v PEG 4000 |
