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| Crystal structure of a putative uncharacterized protein Rv3404c and likely sugar N-formyltransferase from Mycobacterium tuberculosis bound to uridine diphosphate |
| This entry was created with PDB-REDO version 8.18 using the deposited PDB model version 1.2 |
| From original header | |||||
|---|---|---|---|---|---|
| Spacegroup | I 41 3 2 | a: 271.940Å b: 271.940Å c: 271.940Å | α: 90.00° β: 90.00° γ: 90.00° | ||
| Resolution | 2.85 Å | Reflections | 40065 | Test set | 1930 (4.8%) |
| R | 0.1715 | R-free | 0.1937 | ||
| According to PDB-REDO | |||||
| Resolution | 2.85 Å | Reflections | 40065 | Test set | 1930 (4.8%) |
| Twin | false | Radiation damage | 60 | ||
| PDB-REDO files | |||||
| Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
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| Links | |||||
| PDBe | RCSB PDB | Proteopedia | |||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.1752 | 0.1701 |
| R-free | 0.1942 | 0.1916 |
| Bond length RMS Z-score | 0.861 | 0.595 |
| Bond angle RMS Z-score | 0.858 | 0.724 |
| Model quality | ||
| Ramachandran plot normality | -1.686 38 | -1.825 35 |
| Rotamer normality | -1.408 63 | -1.031 71 |
| Coarse packing | 0.909 83 | 0.683 77 |
| Fine packing | 0.129 85 | 0.333 88 |
| MolProbity Clashscore | 4.700 56 | 4.770 55 |
| Hydrogen bond satisfaction | 0.922 79 | 0.900 50 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 9 |
| Side chains built | 8 |
| Waters removed | 5 |
| Peptides flipped | 1 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |