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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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2pdt 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 1 21 1 a: 64.120 Å b: 80.570 Å c: 64.110 Å α: 90.00° β: 90.02° γ: 90.00°
Resolution 2.20 Å Reflections 33147 Test set 2897 (8.7%)
R 0.2340 R-free 0.2660
According to PDB-REDO
Resolution 2.20 Å Reflections 33147 Test set 2897 (8.7%) 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
PDBe RCSB PDB 3D bionotes Proteopedia
Validation metrics from PDB-REDO
Crystallographic refinement
R 0.3024 0.1745
R-free 0.3142 R-free was considered biased, the estimated unbiased R-free was used. 0.2168
Bond length RMS Z-score 0.352 0.566
Bond angle RMS Z-score 0.589 0.756
Model quality (raw scores | percentiles)
Ramachandran plot appearance -2.235 19 0.547 88
Rotamer normality -4.252 8 -1.800 45
Coarse packing -1.220 N/A -0.667 N/A
Fine packing -1.751 17 -0.806 61
Bump severity 0.044 31 0.012 75
Hydrogen bond satisfaction 0.910 62 0.922 78
WHAT_CHECK Report Report
Significant model changes
Description Count
Rotamers changed 9
Side chains flipped 0
Waters removed 143
Peptides flipped 1
Chiralities fixed 0
Residues fitting density better 362
Residues fitting density worse 0
Model quality compared to resolution neighbours
Change in density map fit (RSCC)