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PDB-REDO Databank

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7kdu redone
Ricin bound to VHH antibody V5E4

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 21 1 a: 45.281 Å b: 76.494 Å c: 101.440 Å α: 90.00° β: 90.92° γ: 90.00°
Resolution 2.81 Å Reflections 16830 Test set 879 (5.2%)
R 0.2370 R-free 0.2940
According to PDB-REDO
Resolution 2.81 Å Reflections 16830 Test set 879 (5.2%) Twin false
PDB-REDO files
Re-refined and rebuilt structure
( PDB | mmCIF | MTZ)
Re-refined (only) structure
( PDB | MTZ)
All files
(compressed)
Links
PDBe RCSB PDB 3D bionotes Proteopedia
Validation metrics from PDB-REDO
PDB PDB-REDO
Crystallographic refinement
R 0.2654 0.2631
R-free 0.3078 0.3553
Bond length RMS Z-score 0.259 0.583
Bond angle RMS Z-score 0.539 0.847
Model quality (raw scores | percentiles)
Ramachandran plot appearance -3.384 13 -4.484 7
Rotamer normality -3.039 39 -5.376 12
Coarse packing -0.897 19 -1.205 11
Fine packing -1.260 42 -1.586 28
Bump severity 0.354 3 0.370 2
Hydrogen bond satisfaction 0.783 4 0.804 5
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 2
Side chains flipped 1
Waters removed 23
Peptides flipped 17
Chiralities fixed 0
Residues fitting density better 1
Residues fitting density worse 0
Change in density map fit (RSCC)