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3rzv redone
The Crystal Structure of a E280A Mutant of the Catalytic Domain of AMSH

This information was created with PDB-REDO version 7.0. Please log in to request an update.

Crystallographic data
From PDB header
Spacegroup P 43 21 2 a: 53.437 Å b: 53.437 Å c: 128.828 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 1.67 Å Reflections 22384 Test set 1146 (5.1%)
R 0.1800 R-free 0.2050
According to PDB-REDO
Resolution 1.67 Å Reflections 22384 Test set 1146 (5.1%) 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 0.1760 0.1775
R-free 0.2004 0.2122
Bond length RMS Z-score 0.292 0.707
Bond angle RMS Z-score 0.606 0.888
Model quality (raw scores | percentiles)
Ramachandran plot appearance 1.550 97 1.988 98
Rotamer normality -2.116 38 -1.450 53
Coarse packing -0.153 N/A -0.114 N/A
Fine packing -1.862 14 -1.618 22
Bump severity 0.001 98 0.001 98
Hydrogen bond satisfaction 0.878 32 0.896 46
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 15
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 11
Residues fitting density worse 9
Change in density map fit (RSCC)