| Salmonella typhi PltB Homopentamer N29K Mutant with Neu5Ac-alpha-2-3-Gal-beta-1-4-GlcNAc Glycans |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 2.2 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 21 21 21 | a: 61.053 Å | b: 96.894 Å | c: 119.006 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
| Resolution | 1.77 Å | Reflections | 69142 | Test set | 2000 (2.9%) | ||
| R | 0.1804 | R-free | 0.2033 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.77 Å | Reflections | 69142 | Test set | 2000 (2.9%) | ||
| Twin | false | Radiation damage | 79 | ||||
| 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 | 0.1822 | 0.1784 |
| R-free | 0.2044 | 0.1946 |
| Bond length RMS Z-score | 1.168 | 0.486 |
| Bond angle RMS Z-score | 0.834 | 0.681 |
| Model quality | ||
| Ramachandran plot normality | -0.079 80 | 0.242 87 |
| Rotamer normality | -0.382 84 | 0.409 94 |
| Coarse packing | 1.472 93 | 1.387 92 |
| Fine packing | -0.649 66 | -0.702 65 |
| Bump severity | 0.005 72 | 0.005 72 |
| Hydrogen bond satisfaction | 0.902 53 | 0.910 64 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 10 |
| Side chains built | 0 |
| Waters removed | 0 |
| Peptides flipped | 1 |
| Chiralities fixed | 0 |
| Residues fitting density better | 2 |
| Residues fitting density worse | 0 |