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Structure of human CD1d-sulfatide |
This entry was created with PDB-REDO version 8.03. |
From original header | |||||||
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Spacegroup | P 2 21 21 | a: 40.959 Å | b: 51.576 Å | c: 210.947 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 2.60 Å | Reflections | 14040 | Test set | 700 (5.0%) | ||
R | 0.2208 | R-free | 0.2841 | ||||
According to PDB-REDO | |||||||
Resolution | 2.60 Å | Reflections | 14040 | Test set | 700 (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 | 0.2420 | 0.2071 |
R-free | 0.2932 | 0.2768 |
Bond length RMS Z-score | 0.508 | 0.256 |
Bond angle RMS Z-score | 0.599 | 0.473 |
Model quality | ||
Ramachandran plot normality | -1.700 36 | -1.288 45 |
Rotamer normality | 0.958 98 | -1.445 69 |
Coarse packing | -0.011 61 | 0.224 73 |
Fine packing | -0.542 69 | -0.208 78 |
Bump severity | 0.152 7 | 0.143 8 |
Hydrogen bond satisfaction | 0.918 75 | 0.920 77 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 8 |
Side chains flipped | 15 |
Waters removed | 13 |
Peptides flipped | 3 |
Chiralities fixed | 0 |
Residues fitting density better | 7 |
Residues fitting density worse | 0 |