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Structure of the BG505 SOSIP.664 trimer in complex with neutralizing antibody Fab fragments 10-1074 and BG24 |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
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Spacegroup | H 3 | a: 208.958 Å | b: 208.958 Å | c: 155.914 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
Resolution | 4.00 Å | Reflections | 21372 | Test set | 1250 (5.8%) | ||
R | 0.2455 | R-free | 0.2772 | ||||
According to PDB-REDO | |||||||
Resolution | 4.00 Å | Reflections | 21372 | Test set | 1078 (5.0%) New test set, PDB-REDO compensated for this | ||
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 | 0.3466 | 0.3031 |
R-free | 0.4055 R-free was considered biased, the estimated unbiased R-free was used | 0.3211 |
Bond length RMS Z-score | 1.210 | 0.299 |
Bond angle RMS Z-score | 1.168 | 0.522 |
Model quality | ||
Ramachandran plot normality | -2.641 20 | -4.022 9 |
Rotamer normality | -2.772 44 | -3.154 37 |
Coarse packing | -1.346 8 | -1.380 8 |
Fine packing | -2.688 4 | -2.548 5 |
Bump severity | 0.990 0 | 0.926 0 |
Hydrogen bond satisfaction | 0.755 3 | 0.776 3 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 5 |
Side chains flipped | 0 |
Waters removed | 0 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 99 |
Residues fitting density worse | 60 |