TABLE 3.
Statistics for fitting Fab structures into corresponding cryoEM densitye
| Fabf |
Rcrita
|
Sumfb
|
Clash (%)c
|
−Den (%)d
|
||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Fab | Con | Var | Fab | Con | Var | Fab | Con | Var | Fab | Con | Var | |
| 14 | 4.12 | 1.84 | 4.04 | 58.8 | 61.2 | 60.3 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
| AIF | 0.76 | 3.35 | 1.39 | 55.3 | 54.7 | 58.3 | 0.0 | 0.0 | 0.0 | 0.3 | 0.0 | 0.1 |
| 14/WAM | 3.35 | 56.4 | 0.0 | 0.0 | ||||||||
| B | 3.10 | 5.26 | 3.21 | 36.7 | 38.9 | 33.2 | 0.0 | 0.0 | 1.8 | 4.2 | 0.2 | 6.6 |
| 6 | 2.21 | 2.50 | 1.76 | 21.7 | 10.1 | 30.4 | 0.0 | 0.0 | 0.0 | 2.1 | 4.6 | 3.8 |
| 8 | 3.22 | 6.44 | 2.98 | 52.7 | 50.6 | 51.2 | 0.0 | 0.0 | 0.0 | 1.1 | 0.0 | 2.1 |
| 15 | 3.66 | 6.80 | 5.28 | 48.9 | 47.8 | 52.1 | 0.0 | 0.0 | 0.0 | 1.6 | 0.4 | 2.9 |
| 16 | 4.56 | 1.70 | 3.43 | 45.7 | 48.5 | 46.0 | 0.0 | 0.0 | 0.0 | 5.6 | 0.5 | 5.8 |
| E | 4.12 | 1.90 | 4.11 | 54.9 | 54.5 | 52.6 | 0.0 | 0.0 | 0.0 | 1.2 | 0.1 | 1.7 |
| F | 3.38 | 4.42 | 5.52 | 50.4 | 50.1 | 53.0 | 0.0 | 0.0 | 0.0 | 0.5 | 0.0 | 0.2 |
Rcrit = Σcriteria [(x − mean x)/(RMS from mean x)], where x is the value of each criterion.
Sumf is defined as the average value of density for all nonhydrogen atomic positions normalized by setting the highest density in the map to 100.
Clash represents the percentage of atoms in the model that have steric clashes with symmetry-related subunits.
−Den provides the percentage of atoms that are positioned in negative density.
Each Fab was fit in entirety and as separate constant (Con) and variable (Var) domains.
14 is the X-ray crystal structure. AIF is the murine Fab from virus-neutralizing antibody 730.1.4 (PDB accession no. 1AIF), and 14/WAM is the WAM computer-modeled structure of VH and VL based on the sequence of Fab 14.