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PDB-REDO Databank

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4gnc redone
human SMP30/GNL-1,5-AG complex

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

Crystallographic data
From PDB header
Spacegroup P 1 21 1 a: 64.407 Å b: 50.202 Å c: 86.569 Å α: 90.00° β: 99.65° γ: 90.00°
Resolution 1.75 Å Reflections 54752 Test set 2777 (5.1%)
R 0.1950 R-free 0.2300
According to PDB-REDO
Resolution 1.75 Å Reflections 54752 Test set 2777 (5.1%) 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 0.1983 0.1753
R-free 0.2284 0.2011
Bond length RMS Z-score 0.337 0.577
Bond angle RMS Z-score 0.577 0.763
Model quality (raw scores | percentiles)
Ramachandran plot appearance -1.524 39 -0.891 56
Rotamer normality -1.482 68 -0.630 84
Coarse packing 0.316 76 0.566 85
Fine packing -0.536 70 0.222 86
Bump severity 0.030 29 0.002 87
Hydrogen bond satisfaction 0.902 53 0.895 44
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 7
Side chains flipped 37
Waters removed 2
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 11
Residues fitting density worse 0
Change in density map fit (RSCC)