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PDB-REDO Databank

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2w63 redone

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: 50.020 Å b: 70.267 Å c: 148.913 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 1.90 Å Reflections 40087 Test set 509 (1.3%)
R 0.1820 R-free 0.1900
According to PDB-REDO
Resolution 1.90 Å Reflections 40087 Test set 509 (1.3%) 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 0.2228 0.1810
R-free 0.2622 R-free was considered biased, the estimated unbiased R-free was used. 0.1964
Bond length RMS Z-score 0.543 0.559
Bond angle RMS Z-score 0.629 0.735
Model quality (raw scores | percentiles)
Ramachandran plot appearance -1.066 51 -1.165 48
Rotamer normality -1.402 70 -1.505 68
Coarse packing -0.261 48 -0.355 43
Fine packing -1.472 33 -1.603 27
Bump severity 0.009 61 0.007 67
Hydrogen bond satisfaction 0.887 35 0.882 30
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 15
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 8
Residues fitting density worse 0
Change in density map fit (RSCC)