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 2459 crosslinking restraints combined in 627 restraint groups.
| Linker | Residue 1 | Atom 1 | Residue 2 | Atom 2 | Restraint type | Distance, Å | Count |
|---|---|---|---|---|---|---|---|
| DSS | UNK | CA | UNK | CA | upper bound | 30.0 | 954 |
| DSS | UNK | coarse-grained | UNK | coarse-grained | upper bound | 30.0 | 1240 |
| DSS | LYS | coarse-grained | UNK | coarse-grained | upper bound | 30.0 | 38 |
| DSS | LYS | CA | UNK | CA | upper bound | 30.0 | 16 |
| DSS | LYS | coarse-grained | LYS | coarse-grained | upper bound | 30.0 | 145 |
| DSS | LYS | CA | LYS | CA | upper bound | 30.0 | 40 |
| DSS | HIS | coarse-grained | LYS | coarse-grained | upper bound | 30.0 | 4 |
| DSS | THR | coarse-grained | UNK | coarse-grained | upper bound | 30.0 | 12 |
| DSS | LYS | coarse-grained | THR | coarse-grained | upper bound | 30.0 | 6 |
| DSS | LYS | coarse-grained | MET | coarse-grained | upper bound | 30.0 | 4 |
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=627) |
|---|---|---|---|---|---|---|---|
| 1 | 1 | 1 | 21/21 | All | 80.22 | 19.78 | 627 |
| Self-links/ Ambiguous |
81.79 | 18.21 | 571 | ||||
| Self-links/ Intermolecular |
93.75 | 6.25 | 16 | ||||
| Heteromeric links/ Intermolecular |
38.71 | 61.29 | 31 | ||||
| Self-links/ Intramolecular |
100.00 | 0.00 | 9 | ||||
| 1 | 1 | 2 | 1/1 | All | 70.81 | 29.19 | 627 |
| Self-links/ Ambiguous |
72.85 | 27.15 | 571 | ||||
| Self-links/ Intermolecular |
87.50 | 12.50 | 16 | ||||
| Heteromeric links/ Intermolecular |
16.13 | 83.87 | 31 | ||||
| Self-links/ Intramolecular |
100.00 | 0.00 | 9 |
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.