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
3DNA 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.

5xbz redone
Crystal structure of GH family 81 beta-1,3-glucanase from Rhizomucr miehei complexed with laminaripentaose

This information was created with PDB-REDO version 7.32. Please log in to request an update.

Crystallographic data
From PDB header
Spacegroup P 1 21 1 a: 52.916 Å b: 96.958 Å c: 127.642 Å α: 90.00° β: 93.91° γ: 90.00°
Resolution 2.70 Å Reflections 35185 Test set 1765 (5.0%)
R 0.1740 R-free 0.1900
According to PDB-REDO
Resolution 2.70 Å Reflections 35185 Test set 1765 (5.0%) Twin false
PDB-REDO files
Re-refined and rebuilt structure
( PDB | mmCIF | MTZ)
Re-refined (only) structure
( PDB | MTZ)
All files
(compressed)
Links
PDBe RCSB PDB 3D bionotes Proteopedia
Validation metrics from PDB-REDO
PDB PDB-REDO
Crystallographic refinement
R 0.1809 0.1934
R-free 0.2117 R-free was considered biased, the estimated unbiased R-free was used. 0.2495
Bond length RMS Z-score 0.666 0.567
Bond angle RMS Z-score 0.777 0.740
Model quality (raw scores | percentiles)
Ramachandran plot appearance -4.693 6 -3.071 16
Rotamer normality -4.890 16 -3.233 36
Coarse packing -1.173 12 -0.920 18
Fine packing -1.863 18 -1.440 34
Bump severity 0.049 19 0.030 29
Hydrogen bond satisfaction 0.875 25 0.886 34
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 15
Side chains flipped 29
Waters removed 10
Peptides flipped 4
Chiralities fixed 0
Residues fitting density better 0
Residues fitting density worse 0
Change in density map fit (RSCC)