TABLE 1.
Data collection and refinement statistics for liganded and unliganded structures of lipid A-specific antibodies, A6 and S1–15
| Crystal |
||||||
|---|---|---|---|---|---|---|
| S1–15 BBP | S1–15 unliganded | A6 BBP | A6 unliganded | S1–15 T5a | S1–15 T5 no 5′Pa | |
| PDB codes | 4ODT | 4ODU | 4ODV | 4ODW | 4Z8F | 4Z95 |
| Resolution (Å) | 25.0-1.95 (2.02-1.95) | 30.00-2.29 (2.34-2.29) | 25.0-2.15 (2.23-2.15) | 25.0-2.70 (2.80-2.70) | 25.0-1.75 (1.81-1.75) | 30.00-1.79 (1.85-1.79) |
| Space group | P43212 | P21 | P212121 | P1 | P43212 | P43212 |
| a (Å) | 77.5 | 75.8 | 37.6 | 42.1 | 77.6 | 77.8 |
| b (Å) | 77.5 | 77.6 | 64.3 | 69.2 | 77.6 | 77.8 |
| c (Å) | 156.2 | 72.0 | 154.2 | 69.1 | 156.3 | 156.5 |
| α (°) | 90.0 | 90.0 | 90.0 | 71.0 | 90.0 | 90.0 |
| β (°) | 90.0 | 96.8 | 90.0 | 72.4 | 90.0 | 90.0 |
| γ (°) | 90.0 | 90.0 | 90.0 | 88.3 | 90.0 | 90.0 |
| Volume Å3 | 937500 | 420390 | 372247 | 180558 | 940639 | 946473 |
| Wavelength (Å) | 0.979 | 0.979 | 0.979 | 0.979 | 0.979 | 0.979 |
| Mean B-factor (Å2) | 40.3 | 31.0 | 48.1 | 53.30 | 38.9 | 39.0 |
| Z | 1 | 2 | 1 | 2 | 1 | 1 |
| Unique reflections | 35,329 | 34,731 | 21,015 | 18,489 | 46,712 | 43,755 |
| Redundancy | 15.7 (15.8) | 5.0 (5.1) | 4.9 (4.5) | 2.0 (2.0) | 14.5 (14.5) | 9.9 (10.0) |
| 〈I/σ(I)〉 | 34.1 (4.91) | 24.4 (2.79) | 16.0 (4.13) | 18.2 (1.86) | 36. 0 (5.95) | 37.7 (3.7) |
| Rsym (%) | 8.8 (78.6) | 6.3 (61.5) | 8.5 (40.4) | 4.0 (47.2) | 5.90 (61.0) | 5.3 (74.0) |
| Completeness (%) | 100.0 (100.0) | 100.0 (100.0) | 99.7 (99.1) | 98.1 (98.3) | 99.9 (100.0) | 99.9 (100.0) |
| Protein atoms | 3375 | 6662 | 3338 | 6534 | 3375 | 3375 |
| Solvent atoms | 265 | 300 | 94 | 16 | 208 | 278 |
| Heterogenb atoms | 64 | 10 | 38 | 8 | 101 | 5 |
| Nucleic acids | 0 | 0 | 0 | 0 | 5 | 0 |
| Ramachandran outliers | 0 | 1 | 3 | 0 | 0 | 0 |
| Solvent content (%) | 49.0 | 44.9 | 36.8 | 37.3 | 48.4 | 49.9 |
| Refinement | ||||||
| Rwork (%) | 19.7 | 18.7 | 20.4 | 23.1 | 20.8 | 20.3 |
| Rfree (%) | 22.4 | 23.3 | 24.9 | 25.7 | 24.0 | 23.6 |
| r.m.s. bond lengths (Å) | 0.0091 | 0.010 | 0.011 | 0.011 | 0.0093 | 0.010 |
| r.m.s. bond angles (°) | 1.33 | 1.42 | 1.56 | 1.61 | 1.28 | 1.34 |
a Antigen T5 represents the DNA oligonucleotide 5′P-TTTTT-3′P.
b Heterogen atoms describe nonstandard residues, such as prosthetic groups, inhibitors, carbohydrates, solvents, and ions.