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

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: 51.276 Å b: 100.210 Å c: 54.223 Å α: 90.00° β: 99.46° γ: 90.00°
Resolution 1.90 Å Reflections 39632 Test set 1989 (5.0%)
R 0.1330 R-free 0.1690
According to PDB-REDO
Resolution 1.90 Å Reflections 39632 Test set 1989 (5.0%) 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 0.1386 0.1286
R-free 0.1638 0.1574
Bond length RMS Z-score 0.346 0.599
Bond angle RMS Z-score 0.577 0.768
Model quality (raw scores | percentiles)
Ramachandran plot appearance -1.480 41 -1.506 40
Rotamer normality 0.104 93 -0.400 87
Coarse packing 0.410 80 0.383 79
Fine packing -2.045 13 -2.042 13
Bump severity 0.044 21 0.043 22
Hydrogen bond satisfaction 0.905 57 0.901 52
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 5
Side chains flipped 0
Waters removed 35
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 1
Residues fitting density worse 0
Change in density map fit (RSCC)