Table 1 Data collection and refinement statistics.
From: Molecular basis for integrin adhesion receptor binding to p21-activated kinase 4 (PAK4)
Integrin β5743–774-linker-PAK4cat | Integrin β5743–774-linker-PAK4catD440N,S474E | PAK4cat:Integrin β5760–770 | PAK4catD440N,S474E:Integrin β5760–770 | |
|---|---|---|---|---|
PDB ID: 7S47 | PDB ID: 7S48 | PDB ID: 7S46 | ||
Data collection | ||||
Space group | P63 | P41212 | P41212 | P41212 |
X-ray source and detector | APS 24-ID-E | APS 24-ID-E | APS 24-ID-E | APS 24-ID-E |
ADSC Q315 | ADSC Q315 | EIGER 16 M | EIGER 16 M | |
Wavelength (Å) | 0.97918 | 0.97918 | 0.97918 | 0.97918 |
Unit cell | ||||
a, b, c (Å) | 142.8, 142.8, 62.3 | 62.3, 62.3, 178.6 | 61.7, 61.7, 180.0 | 61.8, 61.8, 178.8 |
α, β, γ (°) | 90, 90, 120 | 90, 90, 90 | 90, 90, 90 | 90, 90, 90 |
Resolution | ||||
Rangea (Å) | 50.0–3.5 (3.63–3.5) | 50.0–2.0 (2.07–2.0) | 50.0–1.9 (1.97–1.9) | 50–2.1 (2.18–2.1) |
No. of unique reflections | 9482 | 24727 | 28444 | 21270 |
Completenessa (%) | 100 (100) | 99.8 (100) | 99.4 (99.7) | 99.9 (100) |
Rpima (%) | 10.1 (651.5) | 5.9 (73.7) | 2.2 (28.8) | 4.0 (45.7) |
CC0.5 (%) (in high resolution bin) | 41.4 | 61.2 | 77.5 | 44.7 |
Mean <I>/<σI>a | 8.8 (1.4) | 16.3 (2.2) | 26.9 (1.9) | 17.5 (1.3) |
Wilson B-factor | 94.2 | 30.7 | 34.3 | 43.2 |
Redundancy | 14.3 (13.5) | 8.8 (8.9) | 11.6 (12.5) | 11.4 (9.3) |
Refinement statistics | ||||
Resolution rangea (Å) | 50–3.5 (3.59–3.5) | 50–2.0 (2.05–2.0) | 50–1.9 (1.95–1.9) | 50–2.1 (2.15–2.1) |
Rfactor (%)a | 21.1 (37.7) | 19.4 (27.1) | 17.9 (27.9) | 18.0 (30.7) |
Free Rfactor (%)a | 24.0 (28.6) | 23.7 (33.3) | 22.2 (31.1) | 22.0 (37.7) |
Free R reflectionsa (%) | 5.4 (3.7) | 5.1 (5.4) | 5.2 (5.7) | 4.9 (5.5) |
Free R reflectionsa, no. | 503 (24) | 1258 (90) | 1475 (110) | 1033 (79) |
Residues built | ||||
PAK4 | A/300-590 | A/300–589 | A/300–589 | A/300–589 |
Integrin β5 tail | B/poly-Ala | B/763–768 | B/762–768 | B/762–770 |
No. water molecules | – | 103 | 119 | 67 |
Mean B-factor (Å2) | ||||
Protein (A) | 99.4 | 25.1 | 30.8 | 35.7 |
AMP-PNP (A) | – | 56.3 | – | 55.5 |
Protein (B) | 97.2 | 45.7 | 85.3 | 79.6 |
H2O | – | 39.7 | 43.8 | 46.0 |
Model statistics | ||||
RMSD bond lengths (Å) | 0.007 | 0.015 | 0.013 | 0.015 |
RMSD bond angles (°) | 1.141 | 1.682 | 1.629 | 1.832 |
Ramachandran plot (%) favored/allowed/disallowed | 94.1/5.9/0 | 98.6/1.4/0 | 97.9/2.1/0 | 97.6/2.4/0 |
