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Crystal structure of the Mycobacterium tuberculosis L,D- transpeptidase-2 (LdtMt2) with peptidoglycan sugar moiety and glutamate |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
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Spacegroup | P 1 21 1 | a: 60.906 Å | b: 93.981 Å | c: 75.539 Å | α: 90.00° | β: 92.97° | γ: 90.00° |
Resolution | 1.58 Å | Reflections | 106008 | Test set | 2008 (1.9%) | ||
R | 0.1654 | R-free | 0.1976 | ||||
According to PDB-REDO | |||||||
Resolution | 1.58 Å | Reflections | 106008 | Test set | 2008 (1.9%) | ||
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 | 0.1741 | 0.1314 |
R-free | 0.2049 | 0.1750 |
Bond length RMS Z-score | 0.710 | 0.519 |
Bond angle RMS Z-score | 0.838 | 0.643 |
Model quality | ||
Ramachandran plot normality | -0.102 78 | 0.165 83 |
Rotamer normality | 0.066 93 | 1.085 98 |
Coarse packing | 0.145 69 | 0.247 74 |
Fine packing | -1.194 45 | -0.795 61 |
Bump severity | 0.004 78 | 0.001 92 |
Hydrogen bond satisfaction | 0.913 68 | 0.927 84 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 7 |
Side chains flipped | 12 |
Waters removed | 157 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 85 |
Residues fitting density worse | 0 |