TABLE 3.
Data collection and structure refinement statisticsa
| Data set | Free form | AVI complex | CAZ complex |
|---|---|---|---|
| Data collection | |||
| Source | Photon Factory BL-17A | Photon Factory BL-17A | Photon Factory BL-17A |
| Wavelength (Å) | 0.9800 | 0.9800 | 0.9800 |
| Space group | P21 | P21 | P21 |
| Unit cell parameters | |||
| Length (Å) | a = 50.6, b = 75.2, c = 103.4 | a = 50.4, b = 73.7, c = 102.1 | a = 50.4, b = 74.1, c = 102.3 |
| Angle (°) | β = 95.1 | β = 94.5 | β = 94.8 |
| Resolution range (Å) | 46.9–1.40 (1.48–1.40) | 46.5–1.60 (1.70–1.60) | 46.7–1.65 (1.75–1.65) |
| No. of observed reflections | 1,039,223 (169,454) | 668,610 (109,167) | 630,466 (100,564) |
| No. of unique reflections | 149,918 (23,824) | 96,869 (15,241) | 89,346 (14,132) |
| Multiplicity | 6.9 (7.1) | 6.9 (7.2) | 7.1 (7.1) |
| Completeness (%) | 98.7 (97.2) | 98.4 (96.3) | 98.1 (96.6) |
| Rmerge (%)b | 4.9 (66.0) | 5.9 (66.6) | 5.7 (77.3) |
| ⟨I/σ (I)⟩ | 18.66 (2.59) | 16.86 (2.45) | 18.84 (2.35) |
| Refinement | |||
| Resolution (Å) | 46.9–1.40 (1.42–1.40) | 37.6–1.60 (1.62–1.60) | 43.7–1.65 (1.67–1.65) |
| No. of reflections used | 149,881 (4,852) | 96,856 (2,991) | 89,321 (2,904) |
| Rwork (%)c | 14.7 (23.1) | 16.7 (23.6) | 16.3 (29.9) |
| Rfree (%)d | 16.8 (25.5) | 18.9 (23.3) | 19.4 (36.8) |
| No. of nonhydrogen atoms | 6,613 | 6,059 | 6,003 |
| Protein | 5,811 | 5,342 | 5,281 |
| Ligands | 110 | 113 | 122 |
| Solvent | 696 | 604 | 600 |
| RMSD from ideality | |||
| Bond length (Å) | 0.004 | 0.005 | 0.009 |
| Bond angle (°) | 0.763 | 0.775 | 0.928 |
| Avg B-factor | 24.8 | 29.5 | 29.4 |
| Protein | 22.8 | 27.9 | 27.8 |
| Ligands | 54.6 | 56.1 | 48.8 |
| Solvent | 37.4 | 39.0 | 39.8 |
| Ramachandran plot | |||
| Favored region (%) | 98.85 | 98.80 | 98.63 |
| Allowed region (%) | 1.15 | 1.20 | 1.37 |
| Outlier region (%) | 0.00 | 0.00 | 0.00 |
| Clashscore | 2.12 | 2.22 | 1.40 |
| PDB ID | 6LC7 | 6LC8 | 6LC9 |
a
Values in parentheses denote the highest-resolution shell.
b
Rmerge = 100 × Σhkl Σi |Ii(hkl) − ⟨I(hkl)⟩|/Σhkl Σi Ii(hkl), where ⟨I(hkl)⟩ is the mean value of I(hkl).
c
Rwork = 100 × Σhkl | |Fo| − |Fc| |/Σhkl |Fo|, where Fo and Fc the observed and calculated structure factors, respectively.
d
Rfree is calculated as for Rwork, but for the test set comprising 5% reflections not used in refinement.