Table 1.
Crystallization, X-ray data collection and refinement statistics
| Organism | Chaetomium thermophilum | Saccharomyces cerevisiae | ||||
|---|---|---|---|---|---|---|
| Construct purified | elF5B(517C) | elF5B(517C) | elF5B(517–970) | elF5B(517–970) | elF5B(399–852) | elF5B(399–852) |
| Construct in structure | elF5B(517C) apo | elF5B(870C) | elF5B(520–970)·GDP | elF5B(517–860)·GTP | elF5B(401–852)·apo | elF5B(401–852)·GDP |
| Crystallization | ||||||
| Condition | 100 mM MES (pH 6.8) 12% PEG 20000 10 mM Na-lactate | 100 mM MES (pH 6.8) 12% PEG 20000 10 mM Na-lactate | 15% PEG 8000 0.5 M Li2SO4 | 100 mM Hepes (pH 7) 13% PEG 4000 100 mM NaOAc | 20% ethylene glycol 5% PEG 3350 20 mM MgCI2 | 8% PEG 8000 0.37 M Li2SO4 |
| Temperature (°C) | 4 | 4 | 20 | 20 | 4 | 10 |
| Data collection | ||||||
| Space group | P3221 | P3121 | P212121 | P21 | P41 | P212121 |
| Unit cell |
a = b = 111.5 Å c = 115.2 Å |
a = b = 98.2 Å c = 97.4 Å |
a = 66.9 Å b = 72.9 Å c = 199.2 Å |
a = 55.4 Å b = 114.8 Å c = 65.9 Å |
a = b = 118.0 Å c = 77.5 Å |
a = 73.6 Å b = 119.5 Å c = 120.7 Å; |
| α = β = 90° γ = 120° |
α = β = 90° γ = 120° |
α = β = γ = 90° | α = 90° β = 102.3° γ = 90° |
α = β = γ = 90° | α = β = γ = 90° | |
| Molecules/asym. unit | 1 | 1 | 2 | 2 | 2 | 2 |
| Resolution (Å) | 2.75 (2.85–2.75) | 3.2 (3.3–3.2) | 2.12 (2.21–2.12) | 1.87 (1.97–1.87) | 1.83 (1.93–1.83) | 3.02 (3.12–3.02) |
| Observed reflections | 168 769 (15,898) | 59 836 (5506) | 288 203 (38,832) | 251 805 (36,887) | 426 259 (62,736) | 108 724 (10 591) |
| Unique reflections | 22 063 (2217) | 9288 (800) | 56 555 (7213) | 66 297 (9605) | 93 360 (13677) | 21 521 (1972) |
| Completeness (%) | 99.9 (100) | 99.8 (100) | 99.7 (99.9) | 99.8 (99.8) | 99.8 (99.9) | 99.2 (99.5) |
| <l>σ | 32.66 (3.29) | 32.12 (4.31) | 17.79 (2.97) | 20.53 (2.38) | 21.05 (3.11) | 23.3 (3.52) |
| Rsym (%) | 3.7 (58.9) | 3.4 (57.4) | 5.6 (63.1) | 4.4 (62.0) | 3.9 (52.5) | 5.3 (60.6) |
| Refinement | ||||||
| Rwork (%) | 19.3 | 19.0 | 21.9 | 16.7 | 16.8 | 24.9 |
| Rfree (%) | 23.8 | 22.0 | 25.2 | 20.6 | 19.4 | 28.7 |
| Rmsd from standard stereochemistry | ||||||
| Bond length (Å) | 0.005 | 0.003 | 0.005 | 0.019 | 0.008 | 0.004 |
| Bond angles (°) | 0.82 | 0.66 | 0.95 | 1.75 | 1.17 | 0.99 |
| Ramachandran plot statistics | ||||||
| Most favored (%) | 98.0 | 98.0 | 98.8 | 98.3 | 98.5 | 97.0 |
| Allowed regions (%) | 2.0 | 2.0 | 1.2 | 1.7 | 1.5 | 3.0 |
| Disallowed regions (%) | 0 | 0 | 0 | 0 | 0 | 0 |
Values in parentheses refer to the highest resolution shell.
Rwork and Rfree factors are calculated using the formula R = ∑ hkl||F(obs)hkl| − |F(calc)hkl|| / ∑ hkl|F(obs)hkl|, where F(obs)hkl and F(calc)hkl are observed and measured structure factors, respectively.
Rwork and Rfree differ in the set of reflections they are calculated from: Rfree is calculated for the test set, whereas Rwork is calculated for the working set.