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PDB-REDO Databank

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7kdm redone
Ricin bound to VHH antibody V5G6

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

Crystallographic data
From PDB header
Spacegroup P 1 a: 44.345 Å b: 77.438 Å c: 101.577 Å α: 89.97° β: 90.18° γ: 89.98°
Resolution 2.30 Å Reflections 57474 Test set 2742 (4.8%)
R 0.1870 R-free 0.2380
According to PDB-REDO
Resolution 2.30 Å Reflections 57474 Test set 2742 (4.8%) 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 0.2066 0.1923
R-free 0.2567 0.2343
Bond length RMS Z-score 0.267 0.411
Bond angle RMS Z-score 0.581 0.651
Model quality (raw scores | percentiles)
Ramachandran plot appearance -1.388 43 -1.112 50
Rotamer normality -3.445 33 -1.071 76
Coarse packing -0.259 48 -0.255 49
Fine packing -0.744 63 -0.339 75
Bump severity 0.371 2 0.328 3
Hydrogen bond satisfaction 0.847 13 0.600 0
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 21
Side chains flipped 1
Waters removed 25
Peptides flipped 7
Chiralities fixed 0
Residues fitting density better 1
Residues fitting density worse 0
Change in density map fit (RSCC)