| Parameters (data collection statistics) . | GDP/AlF4− . | GDP . | GMP-PNP . | |
|---|---|---|---|---|
| SeMet . | Native . | |||
| Cell parameters | ||||
| a (Å) | 75.2 | 76.27 | 228.1 | 76.6 |
| b (Å) | 120.6 | 120.5 | 43.6 | 120.9 |
| c (Å) | 190.1 | 190.2 | 97.6 | 190.5 |
| α, β, γ (°) | 90.0, 90.0, 90.0 | 90.0, 90.0, 90.0 | 90.0, 108.1, 90.0 | 90.0, 90.0, 90.0 |
| Space group | I212121 | I212121 | C2 | I212121 |
| Wavelength used (Å) | 0.9792 | 1.0000 | 1.0000 | 1.0000 |
| Resolution (Å) | 50.00 (3.05) – 3.00 | 50.00 (2.85) – 2.80 | 50.00 (2.42) – 2.30 | 50.00 (2.86) − 2.80 |
| No. of all reflections | 120307 (5,755) | 224,007 (6,499) | 122,150 (18,308) | 139,072 (5,654) |
| No. of unique reflections | 17,527 (872) | 21,774 (942) | 40,802 (5,930) | 19,897 (912) |
| Completeness (%) | 98.7(99.0) | 99.0 (87.5) | 99.1 (99.4) | 99.5 (94.7) |
| Average I/σ (I) | 58.3 (24.4) | 43.9 (4.4) | 10.2 (2.3) | 27.2 (2.9) |
| Rmerge (%)a | 5.7 (10.8) | 8.9 (45.2) | 5.3 (44.3) | 9.3 (58.6) |
| Refinement statistics | ||||
| No. of reflections used (σ(F) > 0) | 20,651 | 38,752 | 18,876 | |
| Rwork (%)b | 25.3 | 22.0 | 24.4 | |
| Rfree (%)b | 30.0 | 29.8 | 30.3 | |
| High resolution shell of Rfree (%)b | 45.0 | 36.9 | 40.0 | |
| High resolution shell of Rwork (%)b | 35.0 | 33.3 | 33.2 | |
| r.m.s.d. bond distance (Å) | 0.018 | 0.015 | 0.013 | |
| r.m.s.d. bond angle (°) | 2.000 | 1.852 | 1.695 | |
| Average B-value (Å2) | 86.6 | 69.2 | 54.7 | |
| No. of protein atoms | 5,446 | 5,327 | 5,348 | |
| No. of ligand atoms | 34 | 58 | 66 | |
| No. of solvent atoms | 126 | 146 | 22 | |
| Ramachandran plot | ||||
| Res. in favored regions (%) | 93.8 | 96.8 | 92.8 | |
| Res. in generously allowed regions (%) | 5.5 | 3.0 | 5.9 | |
| Res. in disallowed regions (%) | 0.7 | 1 | 1.2 | |
| Parameters (data collection statistics) . | GDP/AlF4− . | GDP . | GMP-PNP . | |
|---|---|---|---|---|
| SeMet . | Native . | |||
| Cell parameters | ||||
| a (Å) | 75.2 | 76.27 | 228.1 | 76.6 |
| b (Å) | 120.6 | 120.5 | 43.6 | 120.9 |
| c (Å) | 190.1 | 190.2 | 97.6 | 190.5 |
| α, β, γ (°) | 90.0, 90.0, 90.0 | 90.0, 90.0, 90.0 | 90.0, 108.1, 90.0 | 90.0, 90.0, 90.0 |
| Space group | I212121 | I212121 | C2 | I212121 |
| Wavelength used (Å) | 0.9792 | 1.0000 | 1.0000 | 1.0000 |
| Resolution (Å) | 50.00 (3.05) – 3.00 | 50.00 (2.85) – 2.80 | 50.00 (2.42) – 2.30 | 50.00 (2.86) − 2.80 |
| No. of all reflections | 120307 (5,755) | 224,007 (6,499) | 122,150 (18,308) | 139,072 (5,654) |
| No. of unique reflections | 17,527 (872) | 21,774 (942) | 40,802 (5,930) | 19,897 (912) |
| Completeness (%) | 98.7(99.0) | 99.0 (87.5) | 99.1 (99.4) | 99.5 (94.7) |
| Average I/σ (I) | 58.3 (24.4) | 43.9 (4.4) | 10.2 (2.3) | 27.2 (2.9) |
| Rmerge (%)a | 5.7 (10.8) | 8.9 (45.2) | 5.3 (44.3) | 9.3 (58.6) |
| Refinement statistics | ||||
| No. of reflections used (σ(F) > 0) | 20,651 | 38,752 | 18,876 | |
| Rwork (%)b | 25.3 | 22.0 | 24.4 | |
| Rfree (%)b | 30.0 | 29.8 | 30.3 | |
| High resolution shell of Rfree (%)b | 45.0 | 36.9 | 40.0 | |
| High resolution shell of Rwork (%)b | 35.0 | 33.3 | 33.2 | |
| r.m.s.d. bond distance (Å) | 0.018 | 0.015 | 0.013 | |
| r.m.s.d. bond angle (°) | 2.000 | 1.852 | 1.695 | |
| Average B-value (Å2) | 86.6 | 69.2 | 54.7 | |
| No. of protein atoms | 5,446 | 5,327 | 5,348 | |
| No. of ligand atoms | 34 | 58 | 66 | |
| No. of solvent atoms | 126 | 146 | 22 | |
| Ramachandran plot | ||||
| Res. in favored regions (%) | 93.8 | 96.8 | 92.8 | |
| Res. in generously allowed regions (%) | 5.5 | 3.0 | 5.9 | |
| Res. in disallowed regions (%) | 0.7 | 1 | 1.2 | |
Numbers in parentheses are corresponding values for the highest resolution shell. r.m.s.d., root-mean-square deviation; Res., residues.
Rmerge = ΣhΣl |Iih−<Ih>|/ΣhΣI <Ih>, where <Ih> is the mean of the observations Iih of reflection h.
Rwork = Σ(||Fp(obs)| − |Fp(calc) ||)/Σ |Fp(obs)|; Rfree is an R factor for a preselected subset (5%) of reflections that was not included in refinement.