This entry is not up to date with the most recent version of PDB-REDO.
Please log in
to request an update.
Crystal structure of endoglycoceramidase I from Rhodococ-cus equi in complex with GM1 |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
---|---|---|---|---|---|---|---|
Spacegroup | C 1 2 1 | a: 192.283 Å | b: 48.921 Å | c: 120.227 Å | α: 90.00° | β: 113.95° | γ: 90.00° |
Resolution | 2.15 Å | Reflections | 54739 | Test set | 2776 (5.1%) | ||
R | 0.1670 | R-free | 0.2030 | ||||
According to PDB-REDO | |||||||
Resolution | 2.15 Å | Reflections | 54739 | Test set | 2776 (5.1%) | ||
Twin | false | Radiation damage | N/A | ||||
PDB-REDO files | |||||||
Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
|||||
Links | |||||||
PDBe | RCSB PDB | 3D bionotes | Proteopedia |
Original | PDB-REDO | |
---|---|---|
Crystallographic refinement | ||
R | 0.1680 | 0.1586 |
R-free | 0.2034 | 0.1906 |
Bond length RMS Z-score | 0.834 | 0.567 |
Bond angle RMS Z-score | 0.866 | 0.703 |
Model quality | ||
Ramachandran plot normality | -0.513 67 | -0.115 77 |
Rotamer normality | -1.588 66 | -0.995 77 |
Coarse packing | -0.140 54 | -0.113 56 |
Fine packing | -1.748 22 | -1.635 26 |
Bump severity | 0.019 41 | 0.006 70 |
Hydrogen bond satisfaction | 0.901 52 | 0.905 57 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 15 |
Side chains flipped | 0 |
Waters removed | 2 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |