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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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7kd2 redone
Ricin bound to VHH antibody V11B2

This information was created with PDB-REDO version 7.35. Please log in to request an update.

Crystallographic data
From PDB header
Spacegroup P 21 21 2 a: 77.607 Å b: 99.559 Å c: 111.283 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 2.55 Å Reflections 28754 Test set 1456 (5.1%)
R 0.2270 R-free 0.2800
According to PDB-REDO
Resolution 2.55 Å Reflections 28754 Test set 1456 (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 0.2495 0.2409
R-free 0.2934 0.2977
Bond length RMS Z-score 0.399 0.412
Bond angle RMS Z-score 0.660 0.667
Model quality (raw scores | percentiles)
Ramachandran plot appearance -3.023 16 -3.822 10
Rotamer normality -5.484 11 -3.066 39
Coarse packing -0.537 34 -0.774 24
Fine packing -1.113 48 -1.072 50
Bump severity 0.432 2 0.020 39
Hydrogen bond satisfaction 0.851 14 0.870 22
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 10
Side chains flipped 0
Waters removed 5
Peptides flipped 1
Chiralities fixed 0
Residues fitting density better 1
Residues fitting density worse 0
Change in density map fit (RSCC)