Table 1.
Crystallographic data and refinement statistics
| Mutation | Cys-285, -362, -364, -397 → Ala | WT | Arg-286 → Ala | Glu-390 → Ala | Glu-390 → Ala Arg-286 3 Ala |
|---|---|---|---|---|---|
| PDB ID code | 2FQQ | 2FQR | 2FQS | 2FQU | 2FQV |
| Space group | P3221 | P43212 | P43212 | P43212 | P43212 |
| Cell constants | a = b = 71.04 Å, c = 117.76 Å | a = b = 63.3 Å, c = 161.7 Å | a = b = 62.7 Å, c = 160.0 Å | a = b = 63.3 Å, c = 160.9 Å | a= b = 63.2 Å, c = 142.2 Å |
| X-ray source | Rigaku RU-3R | Rigaku RU-3R | Rigaku RU-3R | Rigaku RU-3R | Rigaku RU-3R |
| Wavelength, Å | 1.54 | 1.54 | 1.54 | 1.54 | 1.54 |
| Resolution, Å* | 20–3.3 (3.41–3.30) | 20–1.8 (1.86–1.80) | 20–2.2 (2.28–2.20) | 20–2.1 (2.18–2.10) | 20–1.9 (1.97–1.90) |
| No. of observations | 11,608 | 109,228 | 61,759 | 77,477 | 73,883 |
| No. of reflections | 5,490 | 31,366 | 16,955 | 19,871 | 23,540 |
| Completeness, %* | 99.3 (99.8) | 97.9 (83.7) | 99.9 (99.8) | 99.9 (99.9) | 91.7 (96.3) |
| Mean l/(σl) | 14.4 (1.5) | 5.6 (1.6) | 5.2 (1.7) | 6.1 (1.2) | 4.2 (2.0) |
| Rmerge on l† | 0.125 (0.495) | 0.064 (0.370) | 0.073 (0.403) | 0.078 (0.377) | 0.093 (0.343) |
| Cutoff criteria | I < −3σ(I) | I < −3σ(I) | I < −3σ(I) | I < −3σ(I) | I < −3σ(I) |
| Model and refinement statistics | |||||
| Resolution range, Å | 20–3.3 | 20–1.8 | 20–2.2 | 20–2.1 | 20–1.9 |
| No. of reflections‡ | 5,225 (247) | 28,476 (1,508) | 15,986 (855) | 18,692 (1,009) | 20,408 (1,109) |
| Completeness, % | 99.5 | 95.6 | 99.3 | 99.1 | 91.4 |
| Cutoff criterion | |F| > 0.0 | |F| > 0.0 | |F| > 0.0 | |F| > 0.0 | |F| > 0.0 |
| No. of residues | 235 | 256 | 256 | 258 | 250 |
| No. of water molecules | 18 | 228 | 147 | 160 | 183 |
| rmsd bond lengths, Å | 0.006 | 0.006 | 0.006 | 0.005 | 0.006 |
| rmsd bond angles, ° | 1.119 | 1.301 | 1.252 | 0.822 | 0.899 |
| Luzzati error, Å | 0.667 | 0.251 | 0.366 | 0.319 | 0.279 |
| Correlation factor§ | 0.792 | 0.935 | 0.904 | 0.924 | 0.915 |
| Rcryst¶ | 24.38 | 20.84 | 23.27 | 22.68 | 22.34 |
| Rfree | 28.02 | 23.57 | 27.01 | 25.85 | 24.91 |
| Ramachandran plot statistics‖ | |||||
| Most favored | 183 (88.4) | 202 (90.2) | 205 (91.5) | 204 (90.3) | 197 (89.5) |
| Additional allowed | 24 (11.6) | 21 (9.4) | 18 (8.0) | 22 (9.7) | 22 (10.0) |
| Generously allowed | 0 (0) | 1 (0.4) | 1 (0.4) | 0 (0.0) | 1 (0.5) |
| Disallowed | 0 (0) | 0 (0.0) | 0 (0.0) | 0 (0.0) | 0 (0.0) |
| Overall G factor** | 0.2 | 0.2 | 0.2 | 0.2 | 0.1 |
rmsd, rms deviation.
*Numbers in parentheses indicate high-resolution shells.
†Rmerge = ΣhklΣi|I(hkl)i − 〈I(hkl)〉|/ΣhklΣi〈I(hkl)i〉.
‡Numbers in parentheses indicate the numbers of reflections used to calculate the Rfree factor.
§Correlation factor between the structure factors and the model as calculated by sfcheck.
¶Rcryst = Σhkl|Fo(hkl) − Fc(hkl)|/Σhkl|Fo(hkl)|, where Fo and Fc are observed and calculated structure factors, respectively.
‖Computed with procheck (27). Numbers in parentheses are percentages.
**Overall G factor is a measure of the overall normality of the structure and is obtained from an average of all the different G factors for each residue in the structure. It is essentially a log-odds score based on the observed distributions of these stereochemical parameters (27).