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Crystal Structure of Human Glycolipid Transfer Protein complexed with 3-O-sulfo-galactosylceramide containing nervonoyl acyl chain (24:1) |
This entry was created with PDB-REDO version 7.00. |
From original header | |||||||
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Spacegroup | C 1 2 1 | a: 74.891 Å | b: 50.060 Å | c: 65.404 Å | α: 90.00° | β: 118.52° | γ: 90.00° |
Resolution | 1.10 Å | Reflections | 85610 | Test set | 4312 (5.0%) | ||
R | 0.1380 | R-free | 0.1570 | ||||
According to PDB-REDO | |||||||
Resolution | 1.10 Å | Reflections | 85610 | Test set | 4312 (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 | |
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Crystallographic refinement | ||
R | 0.1368 | 0.1196 |
R-free | 0.1563 | 0.1441 |
Bond length RMS Z-score | 0.598 | 0.693 |
Bond angle RMS Z-score | 0.750 | 0.836 |
Model quality | ||
Ramachandran plot normality | 0.809 92 | 0.869 93 |
Rotamer normality | 1.098 98 | 1.175 98 |
Coarse packing | 0.480 N/A | 0.517 N/A |
Fine packing | -1.164 43 | -1.049 49 |
Bump severity | 0.002 96 | 0.000 99 |
Hydrogen bond satisfaction | 0.915 69 | 0.936 92 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 7 |
Side chains flipped | 0 |
Waters removed | 54 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 123 |
Residues fitting density worse | 4 |