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PDB-IHM

System for Archiving Integrative Structures

Fit of model to data used for modeling?

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 136 crosslinking restraints combined in 136 restraint groups.

Linker Residue 1 Atom 1 Residue 2 Atom 2 Restraint type Distance, Å Count
BrEtY ALA CB TYR CB upper bound 10.2 1
BrEtY ALA CB ASP CB upper bound 10.2 1
BrEtY ALA CB LYS CB upper bound 10.2 3
BrEtY ALA CB LEU CB upper bound 10.2 1
BrEtY ALA CB VAL CB upper bound 10.2 1
BrEtY ALA CB HIS CB upper bound 10.2 1
BrEtY ALA CB ASN CB upper bound 10.2 1
BrEtY CYS CB THR CB upper bound 10.2 1
BrEtY ASP CB CYS CB upper bound 10.2 2
BrEtY CYS CB PHE CB upper bound 10.2 1
BrEtY CYS CB LYS CB upper bound 10.2 1
BrEtY ASP CB ASP CB upper bound 10.2 1
BrEtY ASP CB PHE CB upper bound 10.2 1
BrEtY ASP CB LYS CB upper bound 10.2 1
BrEtY ASP CB VAL CB upper bound 10.2 1
BrEtY ASP CB GLU CB upper bound 10.2 1
BrEtY GLU CB GLU CB upper bound 10.2 1
BrEtY GLU CB PHE CB upper bound 10.2 1
BrEtY GLU CB LYS CB upper bound 10.2 1
BrEtY GLU CB LEU CB upper bound 10.2 1
BrEtY GLU CB VAL CB upper bound 10.2 1
BrEtY PHE CB TYR CB upper bound 10.2 1
BrEtY ASP CB GLY CB upper bound 10.2 1
BrEtY GLY CB PHE CB upper bound 10.2 1
BrEtY GLY CB VAL CB upper bound 10.2 1
BrEtY GLY CB LYS CB upper bound 10.2 5
BrEtY ASN CB GLY CB upper bound 10.2 1
BrEtY GLY CB PRO CB upper bound 10.2 1
BrEtY ARG CB GLY CB upper bound 10.2 2
BrEtY LEU CB LYS CB upper bound 10.2 3
BrEtY ARG CB LEU CB upper bound 10.2 8
BrEtY LEU CB PRO CB upper bound 10.2 1
BrEtY LYS CB MET CB upper bound 10.2 1
BrEtY ASN CB ASP CB upper bound 10.2 2
BrEtY ASN CB PHE CB upper bound 10.2 1
BrEtY ASN CB LYS CB upper bound 10.2 2
BrEtY ASN CB VAL CB upper bound 10.2 2
BrEtY ASN CB LEU CB upper bound 10.2 1
BrEtY ARG CB ASN CB upper bound 10.2 2
BrEtY LYS CB PRO CB upper bound 10.2 4
BrEtY ARG CB PRO CB upper bound 10.2 8
BrEtY GLN CB PHE CB upper bound 10.2 1
BrEtY GLN CB LYS CB upper bound 10.2 1
BrEtY ARG CB ASP CB upper bound 10.2 1
BrEtY ARG CB PHE CB upper bound 10.2 2
BrEtY ARG CB LYS CB upper bound 10.2 5
BrEtY ARG CB VAL CB upper bound 10.2 4
BrEtY ARG CB HIS CB upper bound 10.2 1
BrEtY ARG CB ARG CB upper bound 10.2 4
BrEtY HIS CB SEP CB upper bound 10.2 2
BrEtY LYS CB SEP CB upper bound 10.2 5
BrEtY PRO CB SEP CB upper bound 10.2 3
BrEtY LYS CB SER CB upper bound 10.2 7
BrEtY PRO CB SER CB upper bound 10.2 3
BrEtY HIS CB SER CB upper bound 10.2 1
BrEtY SER CB SER CB upper bound 10.2 1
BrEtY ASN CB SEP CB upper bound 10.2 1
BrEtY ARG CB SEP CB upper bound 10.2 2
BrEtY ASP CB THR CB upper bound 10.2 1
BrEtY PHE CB THR CB upper bound 10.2 2
BrEtY LYS CB THR CB upper bound 10.2 2
BrEtY LEU CB THR CB upper bound 10.2 1
BrEtY THR CB VAL CB upper bound 10.2 1
BrEtY LYS CB TPO CB upper bound 10.2 2
BrEtY ARG CB THR CB upper bound 10.2 1
BrEtY LYS CB VAL CB upper bound 10.2 2
BrEtY LYS CB TYR CB upper bound 10.2 4
BrEtY ASN CB TYR CB upper bound 10.2 2
BrEtY PRO CB TYR CB upper bound 10.2 2

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=136)
1 1 1 1/1 All 46.77 53.23 124
Heteromeric links/
Intermolecular		 46.77 53.23 124

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.