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Crystal Structure of Human Protocadherin-1 EC1-4 with glycosylation |
This entry was created with PDB-REDO version 8.03. |
From original header | |||||||
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Spacegroup | P 61 2 2 | a: 147.227 Å | b: 147.227 Å | c: 149.366 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
Resolution | 3.15 Å | Reflections | 17100 | Test set | 820 (4.8%) | ||
R | 0.2148 | R-free | 0.2634 | ||||
According to PDB-REDO | |||||||
Resolution | 3.14 Å | Reflections | 17100 | Test set | 820 (4.8%) | ||
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 | 0.2174 | 0.2069 |
R-free | 0.2617 | 0.2538 |
Bond length RMS Z-score | 1.181 | 0.712 |
Bond angle RMS Z-score | 0.856 | 0.933 |
Model quality | ||
Ramachandran plot normality | -4.000 9 | -4.514 7 |
Rotamer normality | -5.732 10 | -6.366 6 |
Coarse packing | -1.386 8 | -1.745 4 |
Fine packing | -1.483 32 | -2.029 14 |
Bump severity | 0.148 7 | 0.170 6 |
Hydrogen bond satisfaction | 0.826 8 | 0.829 9 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 6 |
Side chains flipped | 0 |
Waters removed | 0 |
Peptides flipped | 19 |
Chiralities fixed | 0 |
Residues fitting density better | 16 |
Residues fitting density worse | 11 |