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2g2i redone
A Src-like Inactive Conformation in the Abl Tyrosine Kinase Domain

This information was created with PDB-REDO version 7.36. Please log in to request an update.

Crystallographic data
From PDB header
Spacegroup P 41 21 2 a: 88.457 Å b: 88.457 Å c: 235.625 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 3.12 Å Reflections 18261 Test set 925 (5.1%)
R 0.2490 R-free 0.3080
According to PDB-REDO
Resolution 3.00 Å Reflections 18261 Test set 925 (5.1%) 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 0.2933 0.2084
R-free 0.3404 0.2502
Bond length RMS Z-score 0.378 0.452
Bond angle RMS Z-score 0.768 0.702
Model quality (raw scores | percentiles)
Ramachandran plot appearance -6.404 2 -1.814 33
Rotamer normality -4.773 17 -2.600 47
Coarse packing -1.934 3 -1.525 6
Fine packing -1.457 33 -0.557 69
Bump severity 0.132 8 0.027 32
Hydrogen bond satisfaction 0.818 7 0.838 10
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 4
Side chains flipped 10
Waters removed 0
Peptides flipped 8
Chiralities fixed 0
Residues fitting density better 28
Residues fitting density worse 0
Change in density map fit (RSCC)