Crystal Structure of Glucokinase with bound glucose from Acanthamoeba castellanii |
This entry was created with PDB-REDO version 8.06. |
From original header | |||||||
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Spacegroup | P 1 21 1 | a: 114.990 Å | b: 52.790 Å | c: 52.790 Å | α: 90.00° | β: 118.62° | γ: 90.00° |
Resolution | 2.25 Å | Reflections | 59215 | Test set | 2068 (3.5%) | ||
R | 0.1694 | R-free | 0.2013 | ||||
According to PDB-REDO | |||||||
Resolution | 2.25 Å | Reflections | 59215 | Test set | 2068 (3.5%) | ||
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 | |
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Crystallographic refinement | ||
R | 0.1823 | 0.1747 |
R-free | 0.2103 | 0.2061 |
Bond length RMS Z-score | 0.557 | 0.420 |
Bond angle RMS Z-score | 0.716 | 0.578 |
Model quality | ||
Ramachandran plot normality | -0.370 73 | -0.251 76 |
Rotamer normality | -1.383 64 | -0.669 79 |
Coarse packing | 1.401 92 | 1.381 92 |
Fine packing | -1.291 41 | -1.018 52 |
Bump severity | 0.007 65 | 0.008 62 |
Hydrogen bond satisfaction | 0.813 7 | 0.913 68 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 9 |
Side chains flipped | 15 |
Waters removed | 58 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 1 |
Residues fitting density worse | 0 |