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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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5j7z redone

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

Crystallographic data
From PDB header
Spacegroup C 1 2 1 a: 192.283 Å b: 48.921 Å c: 120.227 Å α: 90.00° β: 113.95° γ: 90.00°
Resolution 2.15 Å Reflections 54739 Test set 2776 (5.1%)
R 0.1670 R-free 0.2030
According to PDB-REDO
Resolution 2.15 Å Reflections 54739 Test set 2776 (5.1%) 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 0.1681 0.1631
R-free 0.2035 0.1921
Bond length RMS Z-score 0.460 0.482
Bond angle RMS Z-score 0.707 0.717
Model quality (raw scores | percentiles)
Ramachandran plot appearance -0.485 68 0.047 81
Rotamer normality -1.598 66 -1.057 76
Coarse packing -0.913 19 -0.895 19
Fine packing -1.707 23 -1.592 28
Bump severity 0.019 41 0.006 70
Hydrogen bond satisfaction 0.902 53 0.909 63
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 16
Side chains flipped 0
Waters removed 2
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 0
Residues fitting density worse 0
Change in density map fit (RSCC)