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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.

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5tcd redone
Human alkaline sphingomyelinase (ENPP7) in complex with phosphocholine

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

Crystallographic data
From PDB header
Spacegroup P 31 2 1 a: 104.223 Å b: 104.223 Å c: 113.893 Å α: 90.00° β: 90.00° γ: 120.00°
Resolution 2.40 Å Reflections 23513 Test set 1916 (8.1%)
R 0.1730 R-free 0.2080
According to PDB-REDO
Resolution 2.40 Å Reflections 23513 Test set 1916 (8.1%) Twin false
PDB-REDO files
Re-refined and rebuilt structure
( PDB | mmCIF | MTZ)
Re-refined (only) structure
( PDB | MTZ)
All files
PDBe RCSB PDB 3D bionotes Proteopedia
Validation metrics from PDB-REDO
Crystallographic refinement
R 0.1899 0.1881
R-free 0.2201 0.2275
Bond length RMS Z-score 0.231 0.449
Bond angle RMS Z-score 0.591 0.732
Model quality (raw scores | percentiles)
Ramachandran plot appearance -1.770 34 -1.485 40
Rotamer normality -1.876 60 -2.511 48
Coarse packing -0.884 20 -0.993 16
Fine packing -2.835 3 -2.673 4
Bump severity 0.842 0 0.173 6
Hydrogen bond satisfaction 0.861 17 0.873 23
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 5
Side chains flipped 0
Waters removed 7
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 0
Residues fitting density worse 1
Change in density map fit (RSCC)