Table 2.
X-ray data collection and structure statistics
Values for the highest-resolution shells are shown in parentheses. r.m.s.d., root mean square deviation; Le, Lewis; EDO, 1,2-ethanediol; BTB, 2-[bis(2-hydroxyethyl)amino]-2-hydroxymethylpropane-1,3-diol; CA, calcium ion; SSRL, Stanford Synchrotron Radiation Lightsource; CLS, Canadian Light Source.
| SpGH29C native | SpGH29CT D171N/E215Q LewisX | SpGH29CT D171N/E215Q LewisY | SpGH29CT D171N/E215Q LewisA | |
|---|---|---|---|---|
| Data collection | ||||
| Beamline | SSRL BL9-2 | SSRL BL11-1 | SSRL BL11-1 | CLS 08B1-1 |
| Wavelength (Å) | 0.97946 | 0.97945 | 0.97945 | 0.9795 |
| Space group | P21 | P21 | P21 | P1 |
| Cell dimensions | ||||
| a, b, c (Å) | 60.9, 117.2, 64.9; β = 90.0° | 70.0, 99.0, 79.1; β = 97.6° | 69.8, 98.4, 79.5; β = 97.3° | 50.0, 68.8, 72.7, α = 76.6°; β = 73.2°, γ = 73.6° |
| Resolution (Å) | 41.50–1.72 (1.82–1.72) | 50.0–1.70 (1.79–1.70) | 27.8–1.62 (1.71–1.62) | 46.54–2.10 (2.16–2.10) |
| Rmerge | 0.082 (0.425) | 0.068 (0.307) | 0.050 (0.337) | 0.062 (0.344) |
| Rpim | 0.031 (0.162) | 0.035 (0.165) | 0.026 (0.183) | 0.062 (0.344) |
| CC 1/2 | 0.998 (0.940) | 0.997 (0.919) | 0.998 (0.882) | 0.998 (0.895) |
| 〈I/σI〉 | 16.1 (4.8) | 13.4 (4.2) | 17.0 (4.7) | 14.1 (3.5) |
| Completeness (%) | 98.0 (96.6) | 96.7 (97.1) | 97.2 (98.4) | 98.0 (96.9) |
| Redundancy | 7.8 (7.8) | 4.4 (4.3) | 4.5 (4.5) | 3.9 (4.0) |
| No. of reflections | 735,056 | 498,568 | 587,623 | 198,020 |
| No. unique | 93,880 | 113,304 | 131,486 | 50,203 |
| Refinement | ||||
| Resolution (Å) | 1.72 | 1.70 | 1.62 | 2.10 |
| Rwork/Rfree | 0.17/0.20 | 0.17/0.21 | 0.17/0.20 | 0.17/0.23 |
| No. of atoms | ||||
| Protein | 3,627 (A), 3,629 (B) | 3,656 (A), 3,630 (B) | 3,713 (A), 3,650 (B) | 3,605 (A), 3,582 (B) |
| Ligand | 2 (CA), 28 (BTB), 32 (EDO) | 36 (LeX-A), 36 (LeX-B), 24 (EDO) | 46 (LeY-A), 46 (LeY-B), 56 (EDO) | 36 (LeA-A), 36 (LeA-B) |
| Water | 913 | 1071 | 1032 | 673 |
| B-factors | ||||
| Protein | 19.9 (A), 19.8 (B) | 16.0 (A), 18.5 (B) | 18.2 (A), 23.0 (B) | 22.6 (A), 22.7 (B) |
| Ligand | 24.9 (CA), 29.4 (BTB), 35.9 (EDO) | 12.5 (LeX-A), 13.9 (LeX-B), 31.0 (EDO) | 16.7 (LeY-A), 19.8 (LeY-B), 39.7 (EDO) | 34.3 (LeA-A), 29.5 (LeA-B) |
| Water | 29.5 | 27.5 | 31.2 | 27.3 |
| r.m.s.d. | ||||
| Bond lengths (Å) | 0.012 | 0.008 | 0.007 | 0.010 |
| Bond angles (°) | 1.637 | 1.433 | 1.423 | 1.374 |
| Ramachandran (%) | ||||
| Preferred | 96.8 | 97.2 | 97.3 | 96.8 |
| Allowed | 3.2 | 2.8 | 2.7 | 3.2 |
| Disallowed | 0.0 | 0.0 | 0.0 | 0.0 |