5.1. SAS ?
Model fits displayed in this section are obtained from SASBDB.
5.1.1. Model versus Experimental Scattering Profiles ?
Experimental (blue) and model (red) scattering profiles are presented as log I(q) vs. q together with error weighted residual difference plot between the experimental and model I(q) vs q. The I(q) is the intensity (preferably in absolute units of cm-1 or arbitrary units) and q is the modulus of the scattering vector. For a good fit, residual values should be equally and randomly spaced around the horizontal axis largely within +/- three standard deviations.
5.1.2. Χ² Goodness of Fit Assessment and 5.1.3. CorMap Test ?
χ² values are a measure of the overall fit of the model to the 1D scattering profile. A model that fits the data within its error estimates will have a χ² value close to one, provided that the dominant errors are the random statistical errors (i.e. no systematic errors) from the SAS measurement that are correctly propagated. Correlation Map (CorMap) test is a variance-covariance analysis on the scattering intensities comparing two (or more) scattering profiles (e.g. model versus experiment or multiple measures from the same sample). The CorMap test complements χ² and importantly is independent of the reported errors. The method assigns a probability (P-value based on a 1-tailed Schilling test) for finding the longest string of experimental data points that lie systematically above (+1) or below (-1) the model profile. The P-value lies between 0 – 1 and a significance threshold is chosen below which the model fit is judged to show systematic deviation from experiment. A typical range statisticians use to indicate significant deviation is 0.01 - 0.05. As implemented in the ATSAS suite, the reported CorMap P-value is green (model fit is good) for P > 0.05, yellow for 0.01 < P < 0.05, and red (model deviates significantly) for P < 0.01.
| SASDB ID | Model | χ² | P-value |
|---|---|---|---|
|
SASDBV9
|
1
|
1.28
|
0.02
|
|
SASDBV9
|
2
|
1.10
|
0.01
|
|
SASDBW9
|
1
|
1.97
|
0.00
|
|
SASDBZ9
|
1
|
1.94
|
0.00
|
|
SASDBX9
|
1
|
2.86
|
0.00
|
|
SASDBY9
|
1
|
2.02
|
0.00
|
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 1071 crosslinking restraints combined in 615 restraint groups.
| Linker | Residue 1 | Atom 1 | Residue 2 | Atom 2 | Restraint type | Distance, Ã… | Count |
|---|---|---|---|---|---|---|---|
| DSS | LYS | coarse-grained | LYS | coarse-grained | upper bound | 26.00 | 916 |
| DSS | LYS | CA | LYS | CA | upper bound | 26.00 | 102 |
| DSS | LYS | coarse-grained | THR | coarse-grained | upper bound | 26.00 | 13 |
| DSS | LYS | coarse-grained | MET | coarse-grained | upper bound | 26.00 | 27 |
| DSS | ASN | coarse-grained | LYS | coarse-grained | upper bound | 26.00 | 2 |
| DSS | ARG | coarse-grained | LYS | coarse-grained | upper bound | 26.00 | 2 |
| DSS | GLN | coarse-grained | LYS | coarse-grained | upper bound | 26.00 | 2 |
| DSS | ALA | coarse-grained | LYS | coarse-grained | upper bound | 26.00 | 2 |
| DSS | LYS | coarse-grained | VAL | coarse-grained | upper bound | 26.00 | 3 |
| DSS | GLN | coarse-grained | MET | coarse-grained | upper bound | 26.00 | 1 |
| DSS | LYS | CA | MET | CA | upper bound | 26.00 | 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=615) |
|---|---|---|---|---|---|---|---|
| 1 | 1 | 1 | 1/5 | All | 87.52 | 12.48 | 609 |
| Self-links/ Intramolecular |
96.67 | 3.33 | 300 | ||||
| Heteromeric links/ Intermolecular |
75.37 | 24.63 | 268 | ||||
| Self-links/ Ambiguous |
100.00 | 0.00 | 37 | ||||
| Self-links/ Intermolecular |
100.00 | 0.00 | 4 | ||||
| 1 | 1 | 2 | 1/1000 | All | Not available | Not available | 0 |
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.