Hosting
The Netherlands Cancer Institute
Funding
NWO logo
Johnson and Johnson logo
West-Life logo
iNEXT logo
Powered by
CCP4 logo
WHAT-IF logo
SDSC logo
YASARA logo
PDB-Care logo
PDB-REDO Databank

The PDB-REDO databank contains optimised versions of existing PDB entries with electron density maps, a description of model changes, and a wealth of model validation data. It is a good starting point for any structural biology project.

All the entries are treated with a consistent protocol that reduces the effects of differences in age, software, and depositors. This makes PDB-REDO a great datatset for large scale structure analysis studies.

Here you can find more information about downloading PDB-REDO databank entries. And here you can find the data usage license.

4rk9 redone

This information was created with PDB-REDO version 7.0. Please log in to request an update.

Crystallographic data
From PDB header
Spacegroup P 21 21 21 a: 74.332 Å b: 85.916 Å c: 132.580 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 2.15 Å Reflections 46946 Test set 1405 (3.0%)
R 0.1940 R-free 0.2720
According to PDB-REDO
Resolution 2.15 Å Reflections 46946 Test set 1405 (3.0%) Twin false
PDB-REDO files
Re-refined and rebuilt structure
( PDB | mmCIF | MTZ)
Re-refined (only) structure
( PDB | MTZ)
YASARA scenes
(for visualisation of the results)
All files
(compressed)
Links
PDBe RCSB PDB 3D bionotes Proteopedia
Validation metrics from PDB-REDO
PDB PDB-REDO
Crystallographic refinement
R 0.1961 0.1999
R-free 0.2734 0.2500
Bond length RMS Z-score 0.404 0.581
Bond angle RMS Z-score 0.604 0.761
Model quality (raw scores | percentiles)
Ramachandran plot appearance -2.014 22 -1.132 41
Rotamer normality -2.906 23 -2.077 39
Coarse packing -0.327 N/A -0.211 N/A
Fine packing -1.696 19 -1.387 32
Bump severity 0.062 22 0.064 21
Hydrogen bond satisfaction 0.875 30 0.866 25
WHAT_CHECK Report Report
Significant model changes
Description Count
Rotamers changed 10
Side chains flipped 4
Waters removed 22
Peptides flipped 4
Chiralities fixed 0
Residues fitting density better 19
Residues fitting density worse 29
Model quality compared to resolution neighbours
Change in density map fit (RSCC)