Table 2.
X-ray crystallography dataset analysis and refinement statistics
| Protein complex | Nanobody 10Z-CEP1641−109 | Nanobody 36Z-CEP1641−109 | Nanobody 36Z-TTBK21074−1087-CEP1641−109 |
|---|---|---|---|
| PDB accession code | 7O06 | 7O0S | 7O3B |
| Beamline | I04 (Diamond) | I04 (Diamond) | I03 (Diamond) |
| Space group | P1211 | I121 | C2221 |
| Wavelength (Å) | 0.97942 | 0.97942 | 0.97625 |
| Monomers in the asymmetric unit | 2 | 1 | 3 |
| Unit cell dimensions (Å, °) | a = 50.9, b = 70.7, c = 62.0, α = 90.00, β = 90.09, γ = 90.00 | a = 38.3, b = 50.6, c = 119.9, α = 90.0, β = 99.0, γ = 90.00 | a = 70.6, b = 127.7, c = 218.9, α = 90.0, β = 90.0, γ = 90.0 |
| Resolution (Å) | 62.0–1.6 | 59.2–1.7 | 61.8–2.4 |
| Completeness (overall/inner/outer shell) (%) | 99.4/99.9/98.9 | 100.0/99.7/100.0 | 98.7/95.7/99.4 |
| Rmerge (overall/inner/outer shell) | 0.097/0.059/1.463 | 0.146/0.105/1.658 | 0.091/0.035/0.705 |
| Rpim (overall/inner/outer shell) | 0.040/0.025/0.627 | 0.061/0.047/0.700 | 0.052/0.018/0.436 |
| Mean I/σI (overall/inner/outer shell) | 9.9/27.0/1.7 | 6.1/18.2/1.0 | 8.6/17.0/2.1 |
| Multiplicity (overall/inner/outer shell) | 6.7/6.1/6.3 | 6.6/5.9/6.5 | 3.8/3.7/3.8 |
| Wilson B-factor (Å2) | 19.2 | 24.9 | 33.5 |
| Number of reflections (used in refinement) | 57,658 (57,454) | 25,042 (24,957) | 38,541 (38,506) |
| Number of atoms | 3,796 | 1,909 | 5,678 |
| Waters | 275 | 150 | 104 |
| Rwork/Rfree (% data used) | 0.1804/0.2108 (5%) | 0.2019/0.2411 (5%) | 0.1894/0.2395 (5%) |
| RMSD from ideal values: bond length/angles (Å/°) | 0.006/0.797 | 0.006/0.813 | 0.004/0.623 |
| Mean B value (Å2) | 28.06 | 31.80 | 55.0 |
| Overall correlation coefficient Fo-Fc/Fo-Fc free |
0.963/0.956 | 0.959/0.936 | 0.933/0.911 |
| Molprobity score | 1.21 | 1.34 | 1.71 |
| Clashscore, all atoms | 2.73 | 3.48 | 4.50 |
| Poor rotamers (%) | 1.83 | 1.05 | 3.34 |
| Ramachandran outliers (%) | 0.00 | 0.00 | 0.00 |
| Ramachandran favored (%) | 98.34 | 97.22 | 97.54 |