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5o9r redone
Crystal structure of ScGas2 in complex with compound 9

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: 50.200 Å b: 71.200 Å c: 150.440 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 1.70 Å Reflections 59931 Test set 1832 (3.1%)
R 0.1950 R-free 0.2120
According to PDB-REDO
Resolution 1.70 Å Reflections 59931 Test set 1831 (3.1%) New test set, PDB-REDO compensated for this. 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 0.1970 0.1478
R-free 0.2499 R-free was considered biased, the estimated unbiased R-free was used. 0.1789
Bond length RMS Z-score 0.382 0.388
Bond angle RMS Z-score 0.622 0.638
Model quality (raw scores | percentiles)
Ramachandran plot appearance -0.847 57 -0.549 66
Rotamer normality -0.451 86 -0.494 86
Coarse packing -0.445 39 -0.421 40
Fine packing -1.634 26 -1.603 27
Bump severity 0.000 96 0.003 82
Hydrogen bond satisfaction 0.900 50 0.897 46
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 29
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 98
Residues fitting density worse 0
Change in density map fit (RSCC)