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Crystal structure of human hypoxanthine-guanine phosphoribosyltransferase in complex with 6-fluoro-3-hydroxy-2-pyrazinecarboxamide (T-705) ribose-5'-monophosphate |
This entry was created with PDB-REDO version 8.07. |
From original header | |||||||
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Spacegroup | I 2 2 2 | a: 46.858 Å | b: 73.400 Å | c: 73.400 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 2.73 Å | Reflections | 5280 | Test set | 528 (10.0%) | ||
R | 0.2481 | R-free | 0.2784 | ||||
According to PDB-REDO | |||||||
Resolution | 2.73 Å | Reflections | 5280 | Test set | 528 (10.0%) | ||
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 | 0.2572 | 0.2539 |
R-free | 0.2961 | 0.3088 |
Bond length RMS Z-score | 0.762 | 0.333 |
Bond angle RMS Z-score | 0.544 | 0.520 |
Model quality | ||
Ramachandran plot normality | -4.743 5 | -3.810 10 |
Rotamer normality | -3.940 19 | -3.772 21 |
Coarse packing | -0.497 27 | -0.442 29 |
Fine packing | -2.095 12 | -1.754 22 |
Bump severity | 0.041 21 | 0.043 20 |
Hydrogen bond satisfaction | 0.849 13 | 0.873 24 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 2 |
Side chains flipped | 7 |
Waters removed | 1 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |