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PDB-REDO Databank

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4js1 redone
crystal structure of human Beta-galactoside alpha-2,6-sialyltransferase 1 in complex with cytidine and phosphate

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

Crystallographic data
From PDB header
Spacegroup P 61 a: 65.292 Å b: 65.292 Å c: 162.232 Å α: 90.00° β: 90.00° γ: 120.00°
Resolution 2.09 Å Reflections 21169 Test set 1086 (5.1%)
R 0.1930 R-free 0.2280
According to PDB-REDO
Resolution 2.09 Å Reflections 21169 Test set 1086 (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 0.2090 0.2137
R-free 0.2380 0.2419
Bond length RMS Z-score 0.359 0.583
Bond angle RMS Z-score 0.618 0.755
Model quality (raw scores | percentiles)
Ramachandran plot appearance -2.850 18 -3.664 11
Rotamer normality -3.520 32 -3.435 33
Coarse packing -1.226 10 -1.343 8
Fine packing -2.770 3 -2.659 4
Bump severity 0.256 4 0.255 4
Hydrogen bond satisfaction 0.863 18 0.849 13
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 3
Side chains flipped 0
Waters removed 18
Peptides flipped 2
Chiralities fixed 0
Residues fitting density better 12
Residues fitting density worse 2
Change in density map fit (RSCC)