| Crystal Structure of a fragment of DC-SIGNR (containg the carbohydrate recognition domain and two repeats of the neck) complexed with Lewis-x. |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 2.1 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 32 2 1 | a: 153.750 Å | b: 153.750 Å | c: 128.702 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
| Resolution | 2.25 Å | Reflections | 73013 | Test set | 6102 (8.4%) | ||
| R | 0.2190 | R-free | 0.2560 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.25 Å | Reflections | 73013 | Test set | 6102 (8.4%) | ||
| Twin | false | Radiation damage | 85 | ||||
| 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 | 0.2180 | 0.2018 |
| R-free | 0.2498 | 0.2273 |
| Bond length RMS Z-score | 0.558 | 0.631 |
| Bond angle RMS Z-score | 0.674 | 0.671 |
| Model quality | ||
| Ramachandran plot normality | -2.827 19 | -1.791 35 |
| Rotamer normality | -1.996 51 | -1.178 68 |
| Coarse packing | 0.340 64 | 0.470 69 |
| Fine packing | -1.436 34 | -0.917 56 |
| Bump severity | 0.011 54 | 0.010 56 |
| Hydrogen bond satisfaction | 0.857 16 | 0.847 13 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 13 |
| Side chains flipped | 10 |
| Waters removed | 33 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 13 |
| Residues fitting density worse | 1 |