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Crystal Structure of D48V mutant of Human Glycolipid Transfer Protein complexed with 3-O-sulfo galactosylceramide containing nervonoyl acyl chain |
This entry was created with PDB-REDO version 7.00. |
From original header | |||||||
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Spacegroup | C 1 2 1 | a: 78.315 Å | b: 47.454 Å | c: 63.257 Å | α: 90.00° | β: 125.47° | γ: 90.00° |
Resolution | 1.50 Å | Reflections | 30217 | Test set | 1469 (4.9%) | ||
R | 0.1540 | R-free | 0.2060 | ||||
According to PDB-REDO | |||||||
Resolution | 1.50 Å | Reflections | 30217 | Test set | 1469 (4.9%) | ||
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 | |
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Crystallographic refinement | ||
R | 0.1485 | 0.1823 |
R-free | 0.1932 | 0.2074 |
Bond length RMS Z-score | 0.519 | 0.675 |
Bond angle RMS Z-score | 0.629 | 0.813 |
Model quality | ||
Ramachandran plot normality | 0.407 86 | 0.398 86 |
Rotamer normality | -1.178 60 | -0.644 73 |
Coarse packing | 0.427 N/A | 0.416 N/A |
Fine packing | -0.465 74 | -0.392 76 |
Bump severity | 0.009 81 | 0.005 90 |
Hydrogen bond satisfaction | 0.919 74 | 0.934 91 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 7 |
Side chains flipped | 0 |
Waters removed | 6 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 49 |