Wild-type sperm whale myoglobin with nitrite |
This entry was created with PDB-REDO version 8.08. |
From original header | |||||||
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Spacegroup | P 6 | a: 90.320 Å | b: 90.320 Å | c: 45.250 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
Resolution | 1.85 Å | Reflections | 18181 | Test set | 928 (5.1%) | ||
R | 0.1482 | R-free | 0.1867 | ||||
According to PDB-REDO | |||||||
Resolution | 1.85 Å | Reflections | 18181 | Test set | 928 (5.1%) | ||
Twin | false | Radiation damage | 19 | ||||
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 | |
---|---|---|
Crystallographic refinement | ||
R | 0.1426 | 0.1374 |
R-free | 0.1778 | 0.1686 |
Bond length RMS Z-score | 2.168 | 0.804 |
Bond angle RMS Z-score | 1.392 | 0.716 |
Model quality | ||
Ramachandran plot normality | -1.034 54 | 0.616 91 |
Rotamer normality | -0.694 78 | 0.687 96 |
Coarse packing | 2.575 99 | 2.506 99 |
Fine packing | 0.378 89 | 0.368 89 |
Bump severity | 0.017 42 | 0.002 85 |
Hydrogen bond satisfaction | 0.944 95 | 0.949 97 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 5 |
Side chains flipped | 0 |
Waters removed | 3 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |