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PDB-REDO Databank

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4pey redone
Structure of the E502A variant of sacteLam55A from Streptomyces sp. SirexAA-E in complex with laminaritriose

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: 49.775 Å b: 100.195 Å c: 53.862 Å α: 90.00° β: 103.49° γ: 90.00°
Resolution 1.50 Å Reflections 81428 Test set 4085 (5.0%)
R 0.1150 R-free 0.1440
According to PDB-REDO
Resolution 1.50 Å Reflections 81428 Test set 4085 (5.0%) 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 0.1156 0.0962
R-free 0.1371 0.1239
Bond length RMS Z-score 0.304 0.519
Bond angle RMS Z-score 0.577 0.767
Model quality (raw scores | percentiles)
Ramachandran plot appearance -1.298 45 -1.220 47
Rotamer normality 0.718 97 0.770 97
Coarse packing 0.408 80 0.374 79
Fine packing -2.127 11 -2.100 12
Bump severity 0.041 22 0.039 23
Hydrogen bond satisfaction 0.898 48 0.897 46
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 2
Side chains flipped 0
Waters removed 67
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 25
Residues fitting density worse 0
Change in density map fit (RSCC)