TABLE 1.
Data collection and refinement statistics for liganded and unliganded Fabs of lipid A specific mAbs S55–3 and S55–5
| Crystal | S55–3 BBP-NAc | S55–3 Unliganded | S55–5 BBP-NAc | S55–5 Unliganded |
|---|---|---|---|---|
| PDB codes | 5DQ9 | 4ODS | 5DQD | 5DQJ |
| Resolution (Å) | 25.0–1.95 (2.02–1.95)a | 25.0–1.94 (2.01–1.94) | 25.0–1.94 (2.01–1.94) | 25.0–2.60 (2.69–2.60) |
| Space group | C2 | C2 | P21212 | P21 |
| a (Å) | 338.1 | 135.6 | 56.4 | 53.6 |
| b (Å) | 52.9 | 44.3 | 64.8 | 139.9 |
| c (Å) | 75.4 | 85.4 | 129.8 | 72.1 |
| α, β, γ (°) | 90,101.0,90 | 90,111.6,90 | 90,90,90 | 90,110.7,90 |
| Volume Å3 | 1.32 × 106 | 4.77 × 105 | 4.74 × 105 | 5.05 × 105 |
| Wavelength (Å) | 0.979 | 0.979 | 0.979 | 0.979 |
| Mean B-factor (Å2) | 39.3 | 27.1 | 23.1 | 67.6 |
| Z | 3 | 1 | 1 | 2 |
| Unique reflections | 89318 | 33590 | 36013 | 30002 |
| Redundancy | 4.1 (4.2) | 3.7 (3.7) | 5.7 (5.7) | 3.7 (3.8) |
| 〈I/σ(I)〉 | 14.4 (3.04) | 18.4 (2.93) | 15.8 (3.93) | 19.7 (2.78) |
| Rsym (%) | 9.20 (57.7)b | 6.10 (42.7) | 11.1 (47.8) | 6.00 (53.7) |
| Completeness (%) | 98.7 (98.7) | 95.3 (92.2) | 100.0 (99.9) | 99.2 (100.0) |
| Protein atoms | 9802 | 3312 | 3359 | 6718 |
| Solvent atoms | 484 | 240 | 395 | 54 |
| Ligand atoms | 111 | 0 | 37 | 0 |
| Ramachandran outliers | 7 | 4 | 2 | 2 |
| Solvent content (%) | 47.0 | 51.0 | 50.3 | 53.4 |
| Refinement | ||||
| Rwork (%) | 21.4 | 18.7 | 17.5 | 19.3 |
| Rfree (%)c | 24.6 | 23.3 | 22.2 | 22.8 |
| rmsd bond lengths (Å) | 0.010 | 0.010 | 0.010 | 0.010 |
| rms bond angles (°) | 1.47 | 1.42 | 1.46 | 1.35 |
a Values in the parentheses refer to the highest resolution shell.
b Rsym = ΣhklΣi|Ihkl, i − (Ihkl)|/Σhkl Σi Ihkl, i, where (Ihkl) is the average of Friedel-related observations (i) of a unique reflection (hkl).
c 5% of reflections were omitted for Rfree calculations.
d r.m.s. is root mean square.