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Crystal structure of endoglycoceramidase I from Rhodococ-cus equi in complex with GM3 |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
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Spacegroup | C 1 2 1 | a: 192.521 Å | b: 49.053 Å | c: 120.135 Å | α: 90.00° | β: 114.19° | γ: 90.00° |
Resolution | 1.91 Å | Reflections | 78664 | Test set | 3947 (5.0%) | ||
R | 0.1671 | R-free | 0.2043 | ||||
According to PDB-REDO | |||||||
Resolution | 1.92 Å | Reflections | 78664 | Test set | 3947 (5.0%) | ||
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 | 0.1657 | 0.1586 |
R-free | 0.2035 | 0.1858 |
Bond length RMS Z-score | 0.918 | 0.425 |
Bond angle RMS Z-score | 0.947 | 0.620 |
Model quality | ||
Ramachandran plot normality | -0.170 76 | 0.130 83 |
Rotamer normality | -0.755 82 | -0.086 91 |
Coarse packing | -0.045 59 | -0.032 60 |
Fine packing | -1.953 15 | -1.969 15 |
Bump severity | 0.008 64 | 0.006 70 |
Hydrogen bond satisfaction | 0.904 56 | 0.909 63 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 17 |
Side chains flipped | 0 |
Waters removed | 5 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 2 |
Residues fitting density worse | 0 |