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| Crystal structure of Agrocybe cylindracea galectin with blood type A antigen tetraose |
| This entry was created with PDB-REDO version 8.04 using the deposited PDB model version 2.2 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 65 | a: 102.921 Å | b: 102.921 Å | c: 74.694 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
| Resolution | 1.35 Å | Reflections | 98506 | Test set | 4914 (5.0%) | ||
| R | 0.1400 | R-free | 0.1559 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.35 Å | Reflections | 98506 | Test set | 4914 (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 | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.1364 | 0.1165 |
| R-free | 0.1521 | 0.1359 |
| Bond length RMS Z-score | 0.635 | 0.726 |
| Bond angle RMS Z-score | 0.639 | 0.764 |
| Model quality | ||
| Ramachandran plot normality | 0.115 82 | 0.130 83 |
| Rotamer normality | 0.173 94 | 0.392 95 |
| Coarse packing | 2.221 99 | 2.207 99 |
| Fine packing | -0.217 78 | -0.166 79 |
| Bump severity | 0.002 87 | 0.001 92 |
| Hydrogen bond satisfaction | 0.909 63 | 0.913 68 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 6 |
| Side chains built | 0 |
| Waters removed | 18 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 54 |
| Residues fitting density worse | 0 |