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5oa2 redone
Crystal structure of ScGas2 in complex with compound 8

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

Crystallographic data
From PDB header
Spacegroup P 21 21 21 a: 71.569 Å b: 139.440 Å c: 161.654 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 2.15 Å Reflections 88533 Test set 2669 (3.0%)
R 0.2110 R-free 0.2480
According to PDB-REDO
Resolution 2.15 Å Reflections 88533 Test set 2669 (3.0%) 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 0.2116 0.1905
R-free 0.2459 0.2199
Bond length RMS Z-score 0.436 0.638
Bond angle RMS Z-score 0.684 0.793
Model quality (raw scores | percentiles)
Ramachandran plot appearance -1.746 35 -1.426 42
Rotamer normality -1.740 63 -1.534 67
Coarse packing -0.529 35 -0.438 39
Fine packing -1.762 21 -1.718 23
Bump severity 0.012 53 0.012 53
Hydrogen bond satisfaction 0.885 33 0.882 30
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 7
Side chains flipped 0
Waters removed 22
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 13
Residues fitting density worse 1
Change in density map fit (RSCC)