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PDB-REDO Databank

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4i9s redone
Crystal Structure of the R111K:R132L:Y134F:T54V:R59W Mutant of the Cellular Retinoic Acid Binding Protein Type II in Complex with All-Trans Retinal at 2.58 Angstrom Resolution

This information was created with PDB-REDO version 7.0. Please log in to request an update.

Crystallographic data
From PDB header
Spacegroup P 31 2 1 a: 56.455 Å b: 56.455 Å c: 108.192 Å α: 90.00° β: 90.00° γ: 120.00°
Resolution 2.58 Å Reflections 6566 Test set 0 (0.0%)
R 0.2240 R-free 0.2880
According to PDB-REDO
Resolution 2.58 Å Reflections 6566 Test set 633 (9.6%) New test set, PDB-REDO compensated for this. 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 0.2317 0.2181
R-free 0.3164 R-free was considered biased, the estimated unbiased R-free was used. 0.2315
Bond length RMS Z-score 0.359 0.374
Bond angle RMS Z-score 0.507 0.603
Model quality (raw scores | percentiles)
Ramachandran plot appearance 0.952 93 1.701 98
Rotamer normality -4.814 5 -3.213 19
Coarse packing 1.223 N/A 1.119 N/A
Fine packing 1.647 98 2.384 99
Bump severity 0.012 75 0.001 98
Hydrogen bond satisfaction 0.929 86 0.946 97
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 2
Side chains flipped 8
Waters removed 9
Peptides flipped 1
Chiralities fixed 0
Residues fitting density better 15
Residues fitting density worse 1
Change in density map fit (RSCC)