Table 1.
Data collection and refinement statistics
| Mutant | WT-uncleaved | T168S | T186V | T219A | T219V | Covalent- intermediate |
|---|---|---|---|---|---|---|
| PDB codes | 4O0C | 4O0D | 4O0E | 4O0F | 4O0G | 4O0H |
| Data collection statistics | ||||||
| X-ray source and detector | LS-CAT ID-G | SERCAT ID-22 | LS-CAT ID-D | Rigaku RU-200 | LS-CAT ID-D | Rigaku RU-200 |
| MARCCD 300 | MARCCD 300 | MARCCD 300 | R-AXIS IV ++ | MARCCD 300 | R-AXIS IV ++ | |
| Wavelength (A) | 0.97856 | 1.00000 | 1.07820 | 1.5418 | 1.07820 | 1.5418 |
| Temperature (K) | 100 | 100 | 100 | 93 | 100 | 93 |
| Resolutiona, b (A) | 1.50 (a30-4.46; b1.59- 1.50) | 1.95 (a30-8.70; b2.00- 1.95) | 1.71 (a30-5.06;b1.81- 1.71) | 1.92 (a30-5.67; b2.04- 1.92) | 2.10 (a30-6.16; b2.22- 2.10) | 1.97 (a30-5.82; b2.09- 1.97) |
| Number of Reflections | ||||||
| Observed | 752752 | 214997 | 330581 | 126398 | 125411 | 129948 |
| Unique | 92426 | 36456 | 62537 | 43516 | 34954 | 38615 |
| Completeness (%) | 99.0 (b94.3) | 82.6 (b71.4) | 98.1 (b93.1) | 96.3 (b87.6) | 97.9 (b96.0) | 91.9 (b80.5) |
| Rsym (%) | 9.2 (a4.2; b34.8) | 10.6 (a6.5; b52.3) | 6.2 (a3.4; b55.9) | 6.0 (a3.0; b37.5) | 9.8 (a3.2; b55.9) | 9.7 (a5.0; b43.5) |
| AverageI/σ(I) | 13.2 (b2.86) | 11.7 (b3.18) | 14.41 (b1.65) | 11.78 (b1.86) | 11.54 (b2.79) | 9.16 (b2.05) |
| Space group | P65 | P65 | P65 | P65 | P65 | P65 |
| Unit cell (A): a=b, c | 59.2, 297.8 | 59.7, 299.7 | 59.3, 298.3 | 59.4, 299.2 | 59.4, 306.8 | 59.6, 298.5 |
| Refinement statistics | ||||||
| Refinement program | REFMAC5 | REFMAC5 | REFMAC5 | REFMAC5 | REFMAC5 | REFMAC5 |
| Twinning fraction | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 |
| Rcryst (%) | 15.4 (b21.0) | 17.8 (b22.0) | 17.5 (b18.8) | 16.7 (b19.4) | 16.8 (b20.1) | 16.8 (b17.8) |
| Rfee (%) | 20.5 (b30.5) | 23.4 (b30.9) | 22.5 (b30.8) | 21.5 (b28.1) | 23.6 (b34.1) | 22.6 (b24.0) |
| Resolution range (A) | 30-1.5 | 30-1.95 | 30-1.71 | 30-1.92 | 30-2.10 | 30-1.97 |
| Protein molecules per a.u. | 2 | 2 | 2 | 2 | 2 | 2 |
| Number of atoms: | ||||||
| Protein (protA, protB) | 2146, 2121 | 2185, 2175 | 2168, 2169 | 2164, 2140 | 2120, 2122 | 2173, 2173 |
| Water molecules | 339 | 216 | 177 | 155 | 152 | 193 |
| Na+ | 5 | 2 | 2 | 4 | 2 | 2 |
| Cl- | 2 | - | - | - | - | - |
| Glycine | - | 4 x 5 | - | 4 x 5 | - | - |
| DMSO | 2 x 4 | - | - | - | - | - |
| R.m.s. deviation from ideal: | ||||||
| Bond length (A) | 0.012 | 0.012 | 0.011 | 0.012 | 0.014 | 0.012 |
| Bond angles (°) | 1.559 | 1.591 | 1.603 | 1.741 | 1.766 | 1.748 |
| Average B-factors (A2) | ||||||
| Protein (protA, protB) | 16.1, 16.0 | 19.8, 19.8 | 26.7, 26.6 | 26.6, 26.8 | 28.7, 29.2 | 25.5, 25.6 |
| Water molecules | 20.5 | 19.7 | 26.7 | 23.9 | 25.7 | 23.9 |
| Na+ | 18.2 | 14.4 | 27.9 | 26.1 | 27.9 | 27.7 |
| Cl- | 25.6 | - | - | - | - | - |
| Glycine | - | 23.5 | - | 28.6 | - | - |
| DMSO | 23.7 | - | - | - | - | - |
| Ramachandran plot (%): | ||||||
| most favored regions | 90.8 | 89.4 | 88.7 | 89.3 | 88.6 | 89.7 |
| additionally allowed regions | 8.8 | 10.0 | 10.7 | 9.9 | 11.0 | 9.7 |
| generously allowed/disallowed regions | 0.4 | 0.6 | 0.6 | 0.8 | 0.4 | 0.6 |
a
Low and
b
High (last) resolution shells in parentheses