TABLE 1.
Data collection and refinement statics
Values in parentheses are for the highest resolution shell of the reciprocal space spherically divided to 20 bins.
| Dataset name | Iodide derivative | Apo | Lactose | 3′-SulfoL | 3′-SL | LNF-III |
|---|---|---|---|---|---|---|
| PDB ID | 3APB | 3AP5 | 3AP4 | 3AP6 | 3AP7 | 3AP9 |
| Beamline | BL38B1 (SPring-8) | NW12 (PF-AR, KEK) | BL38B1 (SPring-8) | BL6A (PF, KEK) | BL5A (PF, KEK) | NW12 (PF-AR, KEK) |
| Cryoprotectant | 30% glycerol | 30% MPDa | 30% glycerol | 30% MPDa | 30% MPDa | |
| Wavelength (Å) | 1.30000 | 1.28000 | 0.92000 | 0.97798 | 1.00000 | 1.00000 |
| Space group | P212121 | P43212 | P1 | P1 | P212121 | P212121 |
| Resolution range (Å) | 38.95–1.95 (2.01–1.95) | 34.02–1.92 (1.97–1.92) | 59.44–2.33 (2.39–2.33) | 32.93–1.58 (1.62–1.58) | 49.94–1.53 (1.57–1.53) | 34.00–1.33 (1.36–1.33) |
| Cell dimensions (Å) | a = 65.59, b = 75.87, c = 77.90 | a = b = 76.06, c = 66.51 | a = 41.53, b = 64.89, c = 71.58 | a = 41.38, b = 65.40, c = 71.69 | a = 46.36, b = 49.92, c = 70.29 | a = 46.42, b = 49.95, c = 70.21 |
| Degree | α = β = γ = 90.00 | α = β = γ = 90.00 | α = 98.41, β = 105.49, γ = 108.66 | α = 98.29, β = 105.43, γ = 108.55 | α = β = γ = 90.00 | α = β = γ = 90.00 |
| Multiplicity | 6.6 (4.3) | 13.5 (9.4) | 1.9 (1.8) | 1.9 (1.9) | 12.8 (8.5) | 7.0 (7.1) |
| Completeness (%) | 99.9 (99.6) | 99.9 (100.0) | 95.5 (76.3) | 94.4 (91.5) | 99.9 (100.0) | 98.7 (97.4) |
| Rmerge (%) | 14.9 (35.4) | 6.4 (23.9) | 4.6 (6.0) | 5.5 (12.1) | 3.4 (19.2) | 4.1 (23.1) |
| I/σ | 44.4 (3.4) | 6.7 (5.4) | 6.5 (3.1) | 14.3 (5.8) | 12.7 (3.8) | 28.8 (9.4) |
| Phasing method | Single-wavelength anomalous dispersion | MR | MR | MR | MR | MR |
| No. of heavy atom binding sites | 19 | |||||
| Overall figure of merit | 0.49 | |||||
| Refinement | ||||||
| R-factor (%) | 20.2 | 20.4 | 19.1 | 20.0 | 16.4 | 15.7 |
| Free R-factor (%) | 24.2 | 23.7 | 25.1 | 24.2 | 18.8 | 17.8 |
| Water molecules | 162 | 116 | 307 | 491 | 222 | 286 |
| Hetero molecules | I−×29 | Cl−×1 | Cl−×3, MPDa×1 | |||
| No. of protein molecules/Asym. | 2 | 1 | 4 | 4 | 1 | 1 |
| Cis peptide bonds | Ile17–Pro18 | Ile17–Pro18 | Ile17–Pro18 | Ile17–Pro18 | Ile17–Pro18 | Ile17–Pro18 |
| Lys57–Pro58 | Lys57–Pro58 | Lys57–Pro58 | Lys57–Pro58 | Lys57–Pro58 | Lys57–Pro58 | |
| R.m.s. deviation bond lengthsb (Å) | 0.012 | 0.008 | 0.009 | 0.011 | 0.009 | 0.007 |
| R.m.s. deviation bond anglesc (deg) | 1.318 | 1.155 | 1.205 | 1.423 | 1.299 | 1.242 |
| Ramachandran plot (%) | ||||||
| Most favored regions | 89.9 | 89.1 | 86.6 | 89.0 | 87.5 | 86.7 |
| Additionally allowed regions | 9.3 | 10.1 | 12.1 | 10.2 | 11.7 | 12.5 |
| Generously allowed regions | 0.4 | 0.8 | 1.2 | 0.6 | 0.8 | 0.8 |
| Disallowed regions | 0.4 | 0.0 | 0.0 | 0.2 | 0.0 | 0.0 |
a 2-Methyl-2,4-pentanediol.
b Root mean square deviation from ideal bond lengths.
c Root mean square deviation from ideal bond angles.