Table 1. Crystallographic data.
Values in parentheses are for the highest resolution shell.
| Data set | Compound 18 | Compound 24 | Compound 26 | Compound 34 | Compound 39 | Compound 50 | Compound 76 | Compound 78 | Compound 86 | Sulfaguanidine |
|---|---|---|---|---|---|---|---|---|---|---|
| PDB entry | 8bc8 | 8bc9 | 8bca | 8bcb | 8bcc | 8bcd | 8bce | 8bcf | 8bcg | 8bch |
| Data collection | ||||||||||
| Wavelength (Å) | 1.0332 | 1.0332 | 1.0332 | 1.0332 | 1.0332 | 1.0332 | 0.9184 | 0.9184 | 0.9184 | 0.9184 |
| Temperature (K) | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
| Space group | P212121 | P212121 | P212121 | P212121 | P212121 | P212121 | P212121 | P212121 | P212121 | C2 |
| a, b, c (Å) | 100.7, 119.2, 187.2 | 99.8, 119.2, 188.3 | 100.4, 119.4, 187.8 | 100.2, 119.2, 186.7 | 100.4, 188.2, 119.4 | 101.1, 121.9, 186.3 | 100.1, 119.1, 188.0 | 99.6, 118.8, 187.0 | 99.9, 118.9, 188.1 | 146.5, 149.8, 141.7 |
| α, β, γ (°) | 90, 90, 90 | 90, 90, 90 | 90, 90, 90 | 90, 90, 90 | 90, 90, 90 | 90, 90, 90 | 90, 90, 90 | 90, 90, 90 | 90, 90, 90 | 90, 120.3, 90 |
| Resolution (Å) | 50.00–2.39 (2.53–2.39) | 50.00–2.30 (2.43–2.30) | 50.00–2.80 (2.97–2.80) | 50.00–2.38 (2.52–2.38) | 50.00–2.35 (2.49–2.35) | 50.00–3.50 (3.71–3.50) | 50.00–2.05 (2.17–2.05) | 50.00–2.42 (2.56–2.42) | 50.00–2.39 (2.53–2.39) | 50.00–2.87 (3.04–2.87) |
| Reflections | ||||||||||
| Unique | 89613 (14187) | 100449 (15822) | 56042 (8857) | 89385 (13922) | 94679 (14864) | 29691 (4699) | 139806 (21677) | 85165 (13518) | 89144 (14027) | 58705 (9524) |
| Completeness (%) | 99.7 (98.9) | 199.6 (98.0) | 99.4 (98.8) | 98.7 (96.4) | 99.6 (98.1) | 99.6 (99.3) | 99.2 (96.2) | 99.9 (99.4) | 99.7 (98.4) | 97.1 (98.4) |
| Multiplicity | 6.7 (6.8) | 6.7 (6.4) | 6.7 (6.8) | 6.7 (6.4) | 6.7 (6.5) | 6.7 (6.9) | 6.5 (5.6) | 10.5 (10.5) | 6.7 (6.9) | 6.8 (6.9) |
| Data quality | ||||||||||
| Intensity 〈I/σ(I)〉 | 9.57 (0.81) | 14.75 (1.48) | 8.05 (0.94) | 9.20 (0.75) | 8.55 (0.95) | 8.10 (0.70) | 13.63 (1.03) | 9.14 (0.83) | 8.68 (0.79) | 10.2 (0.63) |
| R meas † (%) | 16.9 (253.9) | 19.5 (123.8) | 22.0 (207.4) | 18.3 (266.2) | 20.3 (227.1) | 20.7 (286.5) | 9.9 (163.4) | 23.1 (263.6) | 21.5 (262.1) | 20.1 (327.2) |
| CC1/2 ‡ | 99.8 (28.9) | 99.9 (57.0) | 99.6 (37.4) | 99.8 (24.2) | 99.5 (33.1) | 99.8 (30.4) | 99.9 (41.9) | 99.7 (36.5) | 99.6 (28.5) | 20.1 (327.2) |
| Wilson B value (Å2) | 53.2 | 148.8 | 66.5 | 53.2 | 46.8 | 135.1 | 39.9 | 50.9 | 48.3 | 82.7 |
| Refinement | ||||||||||
| Resolution (Å) | 50.00–2.39 (2.44–2.39) | 50.00–2.30 (2.35–2.30) | 50.00–2.80 (2.97–2.80) | 50.00–2.38 (2.43–2.38) | 50.00–2.35 (2.40–2.35) | 50.00–3.50 (3.71–3.50) | 50.00–2.05 (2.17–2.05) | 50.00–2.42 (2.56–2.42) | 50.00–2.39 (2.53–2.39) | 50.00–2.87 (2.94–2.87) |
| Reflections | ||||||||||
| Number | 89597 (5607) | 100439 (6220) | 56033 (3446) | 89373 (5537) | 94667 (5848) | 29675 (2514) | 139459 (8335) | 85152 (5389) | 89138 (5499) | 56190 (3286) |
| Test set (%) | 2.34 | 2.09 | 3.75 | 2.35 | 2.22 | 5.0 | 1.50 | 2.47 | 2.36 | 3.58 |
| R work (%) | 20.7 (32.8) | 19.8 (28.4) | 20.1 (35.7) | 20.7 (34.6) | 21.0 (33.2) | 22.2 (37.6) | 22.3 (41.3) | 21.3 (33.3) | 21.4 (35.00) | 28.2 (60.6) |
| R free (%) | 24.5 (35.8) | 24.9 (34.5) | 25.9 (41.9) | 25.8 (40.0) | 25.8 (39.4) | 28.0 (41.1) | 26.8 (43.3) | 27.5 (37.9) | 26.9 (41.9) | 33.7 (64.0) |
| Asymmetric unit | ||||||||||
| Protein residues | 1987 | 1987 | 1987 | 1984 | 1988 | 1985 | 1982 | 1987 | 1985 | 1722 |
| Ethylene glycols | 17 | 11 | 16 | 16 | 10 | — | 12 | 10 | 9 | — |
| Compounds | 3 | 1 | 2 | 2 | 3 | 1 | 1 | 1 | 1 | 1 |
| Waters | 1331 | 419 | 173 | 214 | 422 | — | 527 | 325 | 336 | 11 |
| Mean temperature factors (Å2) | ||||||||||
| All atoms | 73.6 | 68.4 | 78.7 | 70.8 | 65.6 | 150.5 | 63.4 | 73.9 | 68.2 | 119.7 |
| Macromolecules | 4.1 | 68.8 | 79.1 | 71.1 | 66.1 | 151.2 | 64.2 | 74.3 | 68.6 | 119.8 |
| Ligands | 55.8 | 65.5 | 66.4 | 66.4 | 50.3 | — | 53.1 | 69.6 | 55.9 | 60.9 |
| Compounds | 4.2 | 53.1 | 55.2 | 55.2 | 49.5 | 117.5 | 44.5 | 57.2 | 55.5 | 59.9 |
| Water molecules | 52.4 | 53.4 | 54.9 | 50.4 | 49.8 | — | 48.1 | 52.8 | 49.8 | 53.6 |
| R.m.s.d. from target geometry§ | ||||||||||
| Bond lengths (Å) | 0.009 | 0.008 | 0.006 | 0.008 | 0.006 | 0.004 | 0.009 | 0.005 | 0.007 | 0.003 |
| Bond angles (°) | 1.072 | 0.917 | 0.779 | 0.985 | 0.801 | 0.690 | 0.979 | 0.752 | 0.885 | 0.610 |
| Validation statistics | ||||||||||
| Ramachandran plot, residues in | ||||||||||
| Allowed regions (%) | 4.2 | 3.1 | 3.7 | 3.2 | 2.7 | 4.7 | 3.7 | 3.1 | 4.3 | 5.6 |
| Favoured regions (%) | 95.5 | 96.6 | 96.0 | 96.5 | 97.0 | 94.9 | 97.0 | 96.7 | 95.6 | 94.3 |
| Ramachandran plot Z-score (r.m.s.d.) | ||||||||||
| Whole | −1.79 (0.17) | −1.39 (0.17) | −2.19 (0.16) | −1.93 (0.17) | −1.22 (0.17) | −1.95 (0.17) | −1.74 (0.17) | −1.42 (0.17) | −2.13 (0.16) | −2.58 (0.18) |
| Helix | −1.73 (0.14) | −1.35 (0.15) | −1.61 (0.14) | −1.59 (0.14) | −1.12 (0.15) | −1.37 (0.15) | −1.52 (0.15) | −1.03 (0.15) | −1.84 (0.14) | −1.84 (0.15) |
| Sheet | −0.14 (0.25) | 0.27 (0.25) | −0.73 (0.24) | −0.15 (0.25) | 0.27 (0.25) | −0.39 (0.26) | −0.12 (0.26) | −0.16 (0.25) | −0.17 (0.25) | −0.70 (0.29) |
| Loop | −0.78 (0.22) | −0.81 (0.21) | −1.39 (0.20) | −1.24 (0.21) | −0.77 (0.21) | −1.42 (0.21) | −0.98 (0.21) | −1.02 (0.21) | −1.30 (0.21) | −1.77 (0.22) |
| MolProbity clashscore¶ †† | 9.49 | 7.64 | 9.81 | 7.36 | 7.42 | 12.36 | 9.00 | 8.42 | 8.06 | 12.70 |
| MolProbity score¶ | 2.35 | 2.04 | 2.28 | 2.03 | 2.01 | 1.96 | 2.22 | 2.13 | 2.31 | 2.56 |
| Poor rotamers (%) | 3.1 | 3.4 | 4.6 | 3.3 | 3.8 | 0.0 | 4.0 | 4.1 | 5.6 | 5.5 |
| Cβ deviations (%) | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
†
R
meas(I) =
, where 〈I(hkl)〉 is the mean intensity of symmetry-equivalent reflections hkl, I
i
(hkl) is the intensity of a particular observation of hkl and N(hkl) is the number of redundant observations of reflection hkl (Diederichs & Karplus, 1997 ▸).
‡
CC1/2 =
, where
is the mean error within a half data set (Karplus & Diederichs, 2012 ▸).
§
Root-mean-square deviation.
¶
Calculated with MolProbity (Williams et al., 2018 ▸).
††
Clashscore is the number of serious steric overlaps (>0.4) per 1000 atoms (Williams et al., 2018 ▸).