PDBIHM.org

PDB-IHM

System for Archiving Integrative Structures

2.1. Ensemble information?

This entry consists of 0 distinct ensemble.

2.2. 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 Subunit A A 238 1-238 - 100.00 /
100.00 		Atomic
2 Subunit B B 142 1-142 - 100.00 /
100.00 		Atomic
3 DNA short arm C 13 1-13 - 100.00 /
0.00 		Atomic
4 DNA long arm D 22 1-22 - 100.00 /
0.00 		Atomic

2.3. Datasets used for modeling ?

There are 8 unique datasets used to build the models in this entry.
ID Dataset type Database name Data access code
1
NMR data
BMRB
2
SAS data
SASBDB
3
Experimental model
PDB
4
Experimental model
PDB
5
Comparative model
Not available
Not available
6
Other
Not available
Not available
7
Other
Not available
Not available
Not available
Other
Not available
Not available

2.4. 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
Homolgy Modeling of XPA
MODELLER
Not available
10
False
False
2
1
Extension of C-terminal Helix of XPA
ROSETTA Remodel
Not available
1000
False
False
3
1
Docking of DNA to XPA
HADDOCK
Not available
1000
False
False
4
1
Randomization and Rigid Body Energy Minimization
HADDOCK
Not available
1000
False
False
5
1
Semi-flexible simulated annealing
HADDOCK
Not available
1000
False
False
6
1
Flexible explicit solvent refinement
HADDOCK
Not available
200
False
False
7
1
Stepwise addition of nucleotide linker
ROSETTA stepwise
Not available
100
False
False
There are 4 software packages reported in this entry.
ID Software name Software version Software classification Software location
1
Not available
model building
2
Not available
model building
3
Not available
model building
4
Not available
Not available