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Structure of 14-3-3 gamma R57E mutant bound to GlcNAcylated peptide |
This entry was created with PDB-REDO version 7.31. |
From original header | |||||||
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Spacegroup | P 1 21 1 | a: 76.366 Å | b: 60.000 Å | c: 125.786 Å | α: 90.00° | β: 90.50° | γ: 90.00° |
Resolution | 2.67 Å | Reflections | 31448 | Test set | 2005 (6.4%) | ||
R | 0.2460 | R-free | 0.2810 | ||||
According to PDB-REDO | |||||||
Resolution | 2.67 Å | Reflections | 31448 | Test set | 1147 (3.6%) New test set, PDB-REDO compensated for this | ||
Twin | false | Radiation damage | N/A | ||||
PDB-REDO files | |||||||
Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
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Links | |||||||
PDBe | RCSB PDB | 3D bionotes | Proteopedia |
Original | PDB-REDO | |
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Crystallographic refinement | ||
R | 0.3200 | 0.2068 |
R-free | 0.3043 R-free was considered biased, the estimated unbiased R-free was used | 0.2621 |
Bond length RMS Z-score | 0.205 | 0.444 |
Bond angle RMS Z-score | 0.408 | 0.660 |
Model quality | ||
Ramachandran plot normality | -4.833 6 | -3.353 13 |
Rotamer normality | -2.943 41 | -2.514 48 |
Coarse packing | 1.409 97 | 1.695 99 |
Fine packing | 0.738 93 | 1.291 96 |
Bump severity | 0.186 6 | 0.030 29 |
Hydrogen bond satisfaction | 0.893 41 | 0.907 60 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 11 |
Side chains flipped | 0 |
Waters removed | 15 |
Peptides flipped | 10 |
Chiralities fixed | 0 |
Residues fitting density better | 27 |
Residues fitting density worse | 1 |