Fit of model(s) to crosslinking-MS data
Restraint types
Restraint types are summarized in the table below. Restraints assigned "by-residue" are interpreted as between CA atoms. Restraints between coarse-grained beads are indicated as "coarse-grained". Restraint group represents a set of crosslinking restraints applied collectively in the modeling.
There are 216 crosslinking restraints combined in 216 restraint groups.
| Linker | Residue 1 | Atom 1 | Residue 2 | Atom 2 | Restraint type | Distance, Å | Count |
|---|---|---|---|---|---|---|---|
| DSS | LYS | CA | LYS | CA | upper bound | 21.0 | 115 |
| DSS | LYS | coarse-grained | LYS | coarse-grained | upper bound | 21.0 | 97 |
| DSS | GLY | coarse-grained | LYS | coarse-grained | upper bound | 21.0 | 1 |
| DSS | GLY | CA | LYS | CA | upper bound | 21.0 | 3 |
Distograms of individual restraints
Restraints with identical thresholds are grouped into one plot. Only the best distance per restraint per model group/ensemble is plotted. Inter- and intramolecular (including self-links) restraints are also grouped into one plot. Distance for a restraint between coarse-grained beads is calculated as a minimal distance between shells; if beads intersect, the distance will be reported as 0.0. A bead with the highest available resolution for a given residue is used for the assessment.
Satisfaction of restraints
Satisfaction of restraints is calculated on a restraint group (a set of crosslinking restraints applied collectively in the modeling) level. Satisfaction of a restraint group depends on satisfaction of individual restraints in the group and the conditionality (all/any). A restraint group is considered satisfied, if the condition was met in at least one model of the model group/ensemble. The number of measured restraints can be smaller than the total number of restraint groups if crosslinks involve non-modeled residues. Only deposited models are used for validation right now.
| State group | State | Model group | # of Deposited models/Total | Restraint group type | Satisfied (%) | Violated (%) | Count (Total=216) |
|---|---|---|---|---|---|---|---|
| 1 | 1 | 1 | 1/69 | All | 81.66 | 18.34 | 169 |
| Heteromeric links/ Intermolecular |
67.21 | 32.79 | 61 | ||||
| Self-links/ Intramolecular |
89.81 | 10.19 | 108 | ||||
| 1 | 1 | 2 | 1/131 | All | 80.47 | 19.53 | 169 |
| Heteromeric links/ Intermolecular |
63.93 | 36.07 | 61 | ||||
| Self-links/ Intramolecular |
89.81 | 10.19 | 108 | ||||
| 1 | 2 | 3 | 1/159 | All | 75.17 | 24.83 | 145 |
| Heteromeric links/ Intermolecular |
54.55 | 45.45 | 44 | ||||
| Self-links/ Intramolecular |
84.16 | 15.84 | 101 | ||||
| 1 | 2 | 4 | 1/41 | All | 77.24 | 22.76 | 145 |
| Heteromeric links/ Intermolecular |
63.64 | 36.36 | 44 | ||||
| Self-links/ Intramolecular |
83.17 | 16.83 | 101 |
Per-model satisfaction rates in model groups/ensembles
Every point represents one model in a model group/ensemble. Where possible, boxplots with quartile marks are also plotted.