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5o9q redone
Crystal structure of ScGas2 in complex with compound 6

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: 49.963 Å b: 70.508 Å c: 150.585 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 1.40 Å Reflections 105292 Test set 2910 (2.8%)
R 0.2110 R-free 0.2260
According to PDB-REDO
Resolution 1.40 Å Reflections 105292 Test set 2910 (2.8%) 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 0.2114 0.1388
R-free 0.2260 0.1620
Bond length RMS Z-score 0.339 0.609
Bond angle RMS Z-score 0.572 0.785
Model quality (raw scores | percentiles)
Ramachandran plot appearance -1.141 49 -0.973 54
Rotamer normality -0.641 83 -0.164 90
Coarse packing -0.650 29 -0.544 34
Fine packing -1.858 18 -1.628 26
Bump severity 0.000 96 0.006 70
Hydrogen bond satisfaction 0.891 39 0.899 49
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 4
Side chains flipped 0
Waters removed 35
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 331
Residues fitting density worse 0
Change in density map fit (RSCC)