8YBO
Crystal structure of nanobody SEB-Nb11 bound to staphylococcal enterotoxin B (SEB)
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | SSRF BEAMLINE BL10U2 |
| Synchrotron site | SSRF |
| Beamline | BL10U2 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2023-12-16 |
| Detector | DECTRIS EIGER X 16M |
| Wavelength(s) | 0.979183 |
| Spacegroup name | P 1 21 1 |
| Unit cell lengths | 60.154, 82.956, 83.546 |
| Unit cell angles | 90.00, 97.44, 90.00 |
Refinement procedure
| Resolution | 82.840 - 1.590 |
| R-factor | 0.26229 |
| Rwork | 0.261 |
| R-free | 0.28432 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Data reduction software | XDS |
| Data scaling software | Aimless (0.7.7) |
| Phasing software | PHASER (2.8.3) |
| Refinement software | REFMAC (5.8.0425) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 82.840 | 1.680 |
| High resolution limit [Å] | 1.590 | 1.590 |
| Rmerge | 0.150 | 2.017 |
| Rmeas | 0.166 | 2.264 |
| Rpim | 0.071 | 1.007 |
| Total number of observations | 580443 | 78965 |
| Number of reflections | 108910 | 15853 |
| <I/σ(I)> | 4.1 | 0.7 |
| Completeness [%] | 100.0 | |
| Redundancy | 5.3 | 5 |
| CC(1/2) | 0.993 | 0.209 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION | 293 | 2% v/v TacsimateTM pH 7.0, 0.1 M HEPES pH 7.5, 20% w/v Polyethylene glycol 3,350 |
