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PDB-IHM

System for Archiving Integrative Structures

Ensemble information?

This entry consists of 0 distinct ensemble.

Summary?

This entry consists of 1 model(s). A total of 5 datasets were used to build this entry.

Representation ?

This entry has 1 representation(s).

ID Model(s) Entity ID Molecule name Chain(s) [auth] Total residues Rigid segments Flexible segments Model coverage/
Starting model coverage
(%)		 Scale
1 1 1 Vimentin A 466 - 1-466 100.00 /
100.00 		Atomic
B
C
D

Datasets used for modeling ?

There are 5 unique datasets used to build the models in this entry.
ID Dataset type Database name Data access code
3
Mass Spectrometry data
Not available
Not available
1
3DEM volume
EMDB
2
3DEM volume
Not available
Not available
4
De Novo model
Not available
Not available
5
De Novo model
Not available
Not available

Methodology and software?

This entry is a result of 1 distinct protocol.
Step number Protocol ID Method name Method type Method description Number of computed models Multi state modeling Multi scale modeling
1
1
Molecular dynamics flexible fitting
Molecular dynamics flexible fitting
The vimentin dimer starting model was fitted by molecular dynamics flexible fitting to an elongated version of the electron density map EMD-16844. Spatial restraints derived from chemical crosslinking and from an electron density map indicating the position of the vimentin tail domains were applied in the modelling procedure.
1
False
False
There are 4 software packages reported in this entry.
ID Software name Software version Software classification Software location
1
2.1.2
model building
2
2.00
model docking
3
Not available
molecular dynamics flexible fitting
4
1.15
model visualization