TABLE 4.
Crystallization conditions, data collection, and refinement statistics
ASU indicates asymmetric unit. BisTris is 2-[bis(2-hydroxyethyl)amino]-2-(hydroxymethyl)propane-1,3-diol; CAPS is 3-(cyclohexylamino)propanesulfonic acid.
| BaIMPDHΔL ·IMP·7 | ClpIMPDHΔL·IMP·1 | ClpIMPDHΔL·IMP·2 | CjIMPDHΔS ·IMP·2 | CjIMPDHΔS ·IMP·4 | |
|---|---|---|---|---|---|
| Data collection | |||||
| Space group | P2 | P1 | P43 | P312 | I422 |
| Cell dimensions | |||||
| a, b, c (Å) | 111.43, 56.23, 111.39 | 88.12, 89.25, 99.19 | 77.61, 77.61, 222.73 | 114.46, 114.46, 256.31 | 118.06, 118.06, 435.16 |
| α, β, γ (°) | 90.00, 89.83, 90.00 | 70.81, 72.66, 79.30 | 90.00, 90.00, 90.00 | 90.00, 90.00, 120.00 | 90.0, 90.0, 90.0 |
| Protein molecules/ASU | 4 | 8 | 4 | 4 | 3 |
| Wavelength (Å) | 0.9792 | 0.9792 | 0.9792 | 0.9793 | 0.9793 |
| Resolution (Å)a | 2.30 (2.30-2.34) | 2.90 (2.90-2.95) | 2.80 (2.80-2.85) | 2.50 (2.50-2.54) | 2.40 (2.40-2.44) |
| Unique reflections | 59,534 (2462) | 59,658 (2981) | 32,619 (1635) | 68,101 (3370) | 58,784 (2723) |
| Rmergeb | 0.118 (0.450) | 0.132 (0.749) | 0.104 (0.704) | 0.109 (0.699) | 0.146 (0.706) |
| 〈I/σI〉 | 7.5 (2.2) | 7.6 (1.5) | 9.4 (2.1) | 10.2 (3.0) | 7.3 (2.4) |
| Completeness (%) | 95.7 (79.5) | 98.5 (98.1) | 99.8 (100.0) | 99.9 (99.0) | 96.7 (91.3) |
| Redundancy | 3.1 (2.2) | 2.0 (2.0) | 3.4 (3.4) | 8.8 (6.2) | 9.1 (5.8) |
| Refinement | |||||
| Resolution (Å) | 2.30 (2.30-2.33) | 2.90 (2.89-2.93) | 2.80 (2.79-2.87) | 2.50 (2.50-2.53) | 2.40 (2.40-2.44) |
| Reflections: work/test set | 56,280/2997 | 59,543/3014 | 32,537/1652 | 64,427/3446 | 55,768/2968 |
| Rwork/Rfreec | 0.173 (0.225) | 0.184 (0.243) | 0.173 (0.223) | 0.180 (0.218) | 0172 (0.212) |
| No. of atoms: protein/ligandsd/water | 9723/272/299 | 20361/434/137 | 10037/208/81 | 10595/296/294 | 8026/199/202 |
| Average B factor (Å2): protein/ligands/water | 41.4/47.3/41.3 | 54.8/54.7/35.8 | 62.3/64.6/45.7 | 66.1/70.8/52.1 | 37.2/53.4/35.6 |
| Bond lengths (Å) | 0.008 | 0.003 | 0.003 | 0.008 | 0.008 |
| Bond angles (°) | 1.155 | 0.86 | 0.67 | 1.153 | 1.15 |
| Most favored | 96.4 | 96.05 | 97.03 | 96.2 | 97.1 |
| Outliers | 0.31 | 0.00 | 0.00 | 0.67 | 0.29 |
| PDB code | 4MY8 | 4Q33 | 4Q32 | 4MZ8 | 4MZ1 |
| Crystallization conditions | 0.1 m sodium/potassium phosphate, pH 6.2, 10% PEG 3,000, 16 °C | 5% tacsimate, pH 7.0, 0.1 m HEPES, pH 7.0, 10% PEG MME 5000, 16 °C | 0.1 m ammonium acetate, 0.1 m BisTris, pH 5.5, 17% PEG 10,000, 16 °C | 1.6 m ammonium sulfate, 0.1 m MES, pH 6.5, 10% dioxane, 16 °C | 0.2 m lithium sulfate, 0.1 m CAPS pH, 10.5, 1.2 m sodium/0.8 m potassium phosphate, 16 °C |
| Cryo-protection solution | 25% glycerol | 25% glycerol | 20% glycerol | 20% sucrose | 20% sucrose |
a Values in parentheses correspond to the highest resolution shell.
b Rmerge = ΣhklΣi|Ii(hkl) − 〈I(hkl)〉|/ΣhklΣi|〈Ii(hkl)〉 , where Ii(hkl) is the intensity for the ith measurement of an equivalent reflection with indices h, k, and l.
c R = Σhkl‖Fobs| − |Fcalc‖/Σhkl|Fobs|, where Fobs and Fcalc are observed and calculated structure factors, respectively. Rfree is calculated analogously for the test reflections, which were randomly selected and excluded from the refinement.
d Ligands include all atoms, excluding protein and water atoms.