TABLE 1.
Crystallographic data and refinement statistics for DegSΔPDZ structures
Rsym = ShSj|Ij(h) − 〈I(h)〉|/ShS[j〈I(h)〉 where Ij(h) is the jth reflection of index h and I(h) is the average intensity of all observations of I(h). Rwork = Sh|Fobs(h) − Fcalc(h)‖/Sh|Fobs(h)| calculated over the 95% of the data in the working set. Rfree is equivalent to Rwork except that it is calculated over the 5% of the data assigned to the test set. Numbers in parentheses represent values for the highest resolution bin. r.m.s.d., root mean square deviation.
| Wild type | DFP-modified | H198P | R178A | Q191A | Y162A | Y162A/H198P | T167V/H198P | |
|---|---|---|---|---|---|---|---|---|
| Protein Data Bank code | 3LGI | 3LH3 | 3LGV | 3LGY | 3LH1 | 3LGU | 3LGT | 3LGW |
| Space group | P212121 | P212121 | P212121 | H3 | H3 | H3 | H3 | H3 |
| Unit cell (Å) | a = 70.38, b = 72.76, c = 128.87 | a = 71.53, b = 132.74, c = 231.20 | a = 71.54, b = 133.56, c = 230.27 Å | a = 70.22, b = 70.22, c = 119.23 Å | a = 70.89, b = 70.89, c = 120.84 Å | a = 70.56, b = 70.56, c = 118.32 Å | a = 70.65, b = 70.65, c = 120.05 Å | a = 70.66, b = 70.66, c = 121.03 Å |
| Subunits/asymmetric unit | 3 | 9 | 9 | 1 | 1 | 1 | 1 | 1 |
| Resolution (Å) | 1.65 | 2.35 | 2.73 | 2.70 | 2.51 | 2.46 | 2.69 | 2.50 |
| Wavelength (Å) | 0.97933 | 0.97949 | 1.54178 | 1.54178 | 0.97949 | 1.54178 | 1.54178 | 1.54178 |
| Rsym | 0.069 (0.481) | 0.070 (0.401) | 0.097 (0.502) | 0.058 (0.201) | 0.058 (0.163) | 0.043 (0.131) | 0.035 (0.212) | 0.034 (0.138) |
| Unique reflections | 79450 (2513) | 84470 (2046) | 55770 (2337) | 5394 (2556) | 6637 (905) | 7790 (2648) | 5868 (2933) | 7320 (3759) |
| Completeness (%) | 99.4 (89) | 91.0 (64) | 94.1 (80) | 89.3 (85) | 85.4 (59) | 97.3 (99) | 93.5 (93) | 94.0 (97) |
| Data redundancy | 12.9 (4.2) | 6.4 (5.5) | 5.6 (5.3) | 10.2 (5.6) | 7.1 (5.5) | 5.5 (5.3) | 4.5 (3.7) | 4.2 (2.5) |
| Average I/σI | 35.2 (3.4) | 18.4 (4.6) | 12.8 (3.4) | 33.0 (4.6) | 26.7 (6.7) | 26.9 (5.5) | 25.1 (4.9) | 27.8 (5.5) |
| Rwork (%) | 15.2 (19.5) | 18.5 (20.5) | 22.0 (25.8) | 23.6 (24.2) | 22.2 (29.5) | 21.0 (25.1) | 22.0 (24.5) | 21.2 (22.2) |
| Rfree (%) | 18.2 (22.4) | 22.7 (26.9) | 27.1 (34.5) | 25.2 (29.7) | 25.9 (36.0) | 24.6 (31.2) | 26.2 (32.1) | 24.1 (30.8) |
| Rwork/Rfree (no hydrogen) | 15.9/18.9 | 18.5/22.9 | 21.7/27.0 | 23.5/25.4 | 21.9/25.3 | 20.9/22.6 | 21.6/24.8 | 21.0/24.8 |
| r.m.s.d. bond length (Å) | 0.005 | 0.004 | 0.004 | 0.004 | 0.005 | 0.003 | 0.004 | 0.004 |
| r.m.s.d. bond angle (°) | 1.043 | 0.883 | 0.800 | 0.803 | 0.825 | 0.767 | 0.822 | 0.844 |
| Total atoms including hydrogen | 11199 | 28642 | 27132 | 2599 | 2894 | 2839 | 2666 | 2784 |
| Solvent atoms | 836 | 737 | 211 | 12 | 10 | 28 | 10 | 21 |
| Average B-value | 19.9 | 46.0 | 52.1 | 87.7 | 82.0 | 74.9 | 92.8 | 79.8 |
| Ramachandrana favored/allowed (%) | 99.1/100 | 98.8/100 | 98.2/100 | 98.8/100 | 99.0/100 | 98.3/100 | 98.2/100 | 98.3/100 |
| Favorable rotamersa (%) | 100 | 99.9 | 100 | 100 | 100 | 100 | 100 | 100 |
| All-atom clash scorea | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.36 | 0.0 | 0.0 |
a Allowed/favorable Ramachandran angles, allowed rotamers, and the all-atom clash score (number of steric overlaps ≥0.4 Å/1000 atoms) were calculated using MolProbity (17).