5.2. Crosslinking-MS ?
5.2.1. Restraint types ?
This table summarizes information about crosslinker(s) used for data generation, and how crosslinking information was translated into actual modeling restraints. 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 251 crosslinking restraints combined in 251 restraint groups.
| Linker | Residue 1 | Atom 1 | Residue 2 | Atom 2 | Restraint type | Distance, Å | Count |
|---|---|---|---|---|---|---|---|
| SDA | LYS | CA | PHE | CA | upper bound | 22.00 | 3 |
| SDA | GLU | CA | LYS | CA | upper bound | 22.00 | 44 |
| SDA | LYS | CA | SER | CA | upper bound | 22.00 | 2 |
| SDA | HIS | CA | LYS | CA | upper bound | 22.00 | 6 |
| SDA | LYS | CA | VAL | CA | upper bound | 22.00 | 5 |
| SDA | HIS | coarse-grained | LYS | coarse-grained | upper bound | 22.00 | 9 |
| SDA | LYS | coarse-grained | THR | coarse-grained | upper bound | 22.00 | 5 |
| SDA | GLU | coarse-grained | LYS | coarse-grained | upper bound | 22.00 | 22 |
| SDA | LYS | coarse-grained | TYR | coarse-grained | upper bound | 22.00 | 5 |
| SDA | MET | coarse-grained | SER | coarse-grained | upper bound | 22.00 | 1 |
| SDA | LYS | CA | TYR | CA | upper bound | 22.00 | 14 |
| SDA | ALA | CA | LYS | CA | upper bound | 22.00 | 4 |
| SDA | GLN | CA | LYS | CA | upper bound | 22.00 | 2 |
| SDA | PRO | coarse-grained | THR | coarse-grained | upper bound | 22.00 | 2 |
| SDA | GLU | coarse-grained | SER | coarse-grained | upper bound | 22.00 | 9 |
| SDA | GLU | coarse-grained | THR | coarse-grained | upper bound | 22.00 | 5 |
| SDA | ALA | coarse-grained | LYS | coarse-grained | upper bound | 22.00 | 9 |
| SDA | GLY | CA | SER | CA | upper bound | 22.00 | 1 |
| SDA | GLY | CA | PRO | CA | upper bound | 22.00 | 2 |
| SDA | LYS | coarse-grained | SER | coarse-grained | upper bound | 22.00 | 10 |
| SDA | GLU | CA | GLY | CA | upper bound | 22.00 | 6 |
| SDA | ASP | coarse-grained | LYS | coarse-grained | upper bound | 22.00 | 4 |
| SDA | LEU | coarse-grained | LYS | coarse-grained | upper bound | 22.00 | 10 |
| SDA | GLU | CA | MET | CA | upper bound | 22.00 | 2 |
| SDA | ALA | coarse-grained | TYR | coarse-grained | upper bound | 22.00 | 1 |
| SDA | MET | CA | TYR | CA | upper bound | 22.00 | 1 |
| SDA | LYS | CA | PRO | CA | upper bound | 22.00 | 4 |
| SDA | GLY | coarse-grained | LYS | coarse-grained | upper bound | 22.00 | 4 |
| SDA | LYS | CA | TRP | CA | upper bound | 22.00 | 1 |
| SDA | PRO | CA | TYR | CA | upper bound | 22.00 | 3 |
| SDA | SER | CA | TYR | CA | upper bound | 22.00 | 1 |
| SDA | LYS | coarse-grained | PRO | coarse-grained | upper bound | 22.00 | 4 |
| SDA | LEU | CA | LYS | CA | upper bound | 22.00 | 5 |
| SDA | GLY | CA | TYR | CA | upper bound | 22.00 | 2 |
| SDA | SER | coarse-grained | TYR | coarse-grained | upper bound | 22.00 | 2 |
| SDA | GLY | CA | LYS | CA | upper bound | 22.00 | 1 |
| SDA | LYS | CA | LYS | CA | upper bound | 22.00 | 3 |
| SDA | THR | coarse-grained | VAL | coarse-grained | upper bound | 22.00 | 2 |
| SDA | MET | CA | PRO | CA | upper bound | 22.00 | 1 |
| SDA | LYS | coarse-grained | PHE | coarse-grained | upper bound | 22.00 | 2 |
| SDA | HIS | CA | TYR | CA | upper bound | 22.00 | 1 |
| SDA | GLU | CA | SER | CA | upper bound | 22.00 | 2 |
| SDA | ILE | CA | LYS | CA | upper bound | 22.00 | 5 |
| SDA | GLU | coarse-grained | GLY | coarse-grained | upper bound | 22.00 | 1 |
| SDA | LEU | CA | TYR | CA | upper bound | 22.00 | 1 |
| SDA | HIS | coarse-grained | THR | coarse-grained | upper bound | 22.00 | 1 |
| SDA | GLU | coarse-grained | MET | coarse-grained | upper bound | 22.00 | 1 |
| SDA | GLN | coarse-grained | LYS | coarse-grained | upper bound | 22.00 | 4 |
| SDA | LYS | coarse-grained | LYS | coarse-grained | upper bound | 22.00 | 2 |
| SDA | LYS | coarse-grained | VAL | coarse-grained | upper bound | 22.00 | 3 |
| SDA | GLY | coarse-grained | TYR | coarse-grained | upper bound | 22.00 | 1 |
| SDA | ASP | CA | TYR | CA | upper bound | 22.00 | 1 |
| SDA | ASP | CA | LYS | CA | upper bound | 22.00 | 2 |
| SDA | ARG | coarse-grained | LYS | coarse-grained | upper bound | 22.00 | 1 |
| SDA | ASN | coarse-grained | LYS | coarse-grained | upper bound | 22.00 | 1 |
| SDA | LYS | coarse-grained | MET | coarse-grained | upper bound | 22.00 | 1 |
| SDA | MET | coarse-grained | TYR | coarse-grained | upper bound | 22.00 | 1 |
| SDA | GLU | coarse-grained | TYR | coarse-grained | upper bound | 22.00 | 1 |
| SDA | GLY | CA | PHE | CA | upper bound | 22.00 | 1 |
| SDA | ASP | CA | SER | CA | upper bound | 22.00 | 1 |
Distograms of individual restraints
Distograms (i.e., histogram plots of distances) provide an overview of distributions of distances between residues for which chemical crosslinks were identified. The shift of the distogram relative to the threshold value may indicate a poor model. 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.
5.2.2. 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=251) |
|---|---|---|---|---|---|---|---|
| 1 | 1 | 1 | 1/5766 | All | 80.88 | 19.12 | 251 |
| Self-links/ Intramolecular |
84.09 | 15.91 | 176 | ||||
| Heteromeric links/ Intermolecular |
73.33 | 26.67 | 75 |
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.
5.3. 3DEM
This section describes fit of models to the 3DEM data. Only results for the representative model, selected as a first model with the largest number of asymmetric units.
3DEM validation for coarse-grained structures is under development.