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Structure of the PBP MelB (Atu4661) in complex with raffinose from A.fabrum C58 |
This entry was created with PDB-REDO version 7.32. |
From original header | |||||||
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Spacegroup | C 1 2 1 | a: 354.300 Å | b: 74.270 Å | c: 108.220 Å | α: 90.00° | β: 105.50° | γ: 90.00° |
Resolution | 2.04 Å | Reflections | 170869 | Test set | 8544 (5.0%) | ||
R | 0.1740 | R-free | 0.2000 | ||||
According to PDB-REDO | |||||||
Resolution | 2.04 Å | Reflections | 170869 | Test set | 8544 (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 | 0.1760 | 0.1713 |
R-free | 0.1991 | 0.1986 |
Bond length RMS Z-score | 0.624 | 0.579 |
Bond angle RMS Z-score | 0.861 | 0.738 |
Model quality | ||
Ramachandran plot normality | -1.256 46 | -1.058 51 |
Rotamer normality | -1.472 68 | -0.690 83 |
Coarse packing | -1.506 6 | -1.485 6 |
Fine packing | -2.545 5 | -2.675 4 |
Bump severity | 0.028 31 | 0.051 19 |
Hydrogen bond satisfaction | 0.625 1 | 0.876 25 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 51 |
Side chains flipped | 0 |
Waters removed | 36 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 5 |
Residues fitting density worse | 0 |