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PDB-REDO Databank

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2w62 redone
Saccharomyces cerevisiae Gas2p in complex with laminaripentaose

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: 50.039 Å b: 70.841 Å c: 149.149 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 1.85 Å Reflections 45861 Test set 555 (1.2%)
R 0.1830 R-free 0.2100
According to PDB-REDO
Resolution 1.85 Å Reflections 45861 Test set 555 (1.2%) 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 0.2331 0.1750
R-free 0.2730 R-free was considered biased, the estimated unbiased R-free was used. 0.1938
Bond length RMS Z-score 0.521 0.559
Bond angle RMS Z-score 0.621 0.708
Model quality (raw scores | percentiles)
Ramachandran plot appearance -1.297 45 -1.700 36
Rotamer normality -1.282 72 -1.068 76
Coarse packing -0.444 39 -0.487 37
Fine packing -1.736 22 -1.636 26
Bump severity 0.005 74 0.002 87
Hydrogen bond satisfaction 0.879 28 0.884 32
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 3
Side chains flipped 0
Waters removed 12
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 35
Residues fitting density worse 0
Change in density map fit (RSCC)