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Crystal structure of myoglobin reconstituted with 6-methyl-6- depropionatehemin |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
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Spacegroup | P 6 | a: 90.248 Å | b: 90.248 Å | c: 45.346 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
Resolution | 1.10 Å | Reflections | 85307 | Test set | 4280 (5.0%) | ||
R | N/A | R-free | N/A | ||||
According to PDB-REDO | |||||||
Resolution | 1.10 Å | Reflections | 85307 | Test set | 4275 (5.0%) 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 | 0.1255 | 0.1392 |
R-free | 0.1406 R-free was considered biased, the estimated unbiased R-free was used | 0.1491 |
Bond length RMS Z-score | 1.360 | 0.937 |
Bond angle RMS Z-score | 1.748 | 1.384 |
Model quality | ||
Ramachandran plot normality | 0.621 90 | 0.711 91 |
Rotamer normality | 0.903 98 | 1.566 99 |
Coarse packing | 2.639 100 | 2.639 100 |
Fine packing | 0.011 83 | 0.219 86 |
Bump severity | 0.007 67 | 0.004 78 |
Hydrogen bond satisfaction | 0.935 90 | 0.944 95 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 2 |
Side chains flipped | 0 |
Waters removed | 32 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 4 |
Residues fitting density worse | 27 |