Table 2.
Lattice and refinement statistics. Fitting of the polypeptide chain into the 2.3 Å MAD-phased electron density map was done with the graphics program O (32). After iterative model building and refinement, the model was refined against both the native and selenomethionyl protein crystal data in space group I222 (crystal form type I). A second crystal form (type 2) was also obtained using the same crystallization conditions. Although the cell constants appeared similar to those of the first crystal form, this crystal form belongs to the space group P21212 without body-centered symmetry. The typical diffraction limit of these crystals was about 2.8 Å. The structure was solved by molecular replacement with AMORE (53) with the protein model determined from the type 1 crystals and was refined to 2.8 Å.
| Type 1 Native | Type 1 Selenomethionine (λ1) | Type 2 Native | |
|---|---|---|---|
| Lattice | |||
| Space group | I222 | I222 | P21212 |
| Cell constants | a=94.4 Å | a=94.5 Å | a=96.4 Å |
| b = 116.7 | b = 116.6 | b = 117.0 | |
| c=37.3 | c=37.2 | c=36.2 | |
| Za* | 1 | 1 | 2 |
| Diffraction data | |||
| dmin | 2.0 Å | 2.0 Å | 2.8 Å |
| RSym1 †(RSym2) (%)† | 5.6 (14.3) | 5.2 (18.5) | 4.3% (11.6) |
| Completeness‡ | 91.5 (60.6) | 94.9 (84.6) | 85.2% (61.6) |
| Total reflections (N) | 57,907 | 59,575 | 23,005 |
| Unique reflections (N) | 13,127 | 13,579 | 9,117 |
| R value (|F|>2σ) (%)§ | 19.3 | 20.6 | 22.5 |
| Rfree(%) | 27.4 | 28.8 | 30.9 |
| Model parameter | |||
| Total non-H atoms | 1629 | 1703 | 2971 |
| Total solvent molecules | 224 | 225 | 28 |
| rms bond length (Å), angle (°) | 0.008, 1.26° | 0.008, 1.30° | 0.010, 2.1° |
| Average B factor (Å) | 22.5 | 23.3 | 30.3 |
| Main-chain rms B (bond, angle) | 1.3, 1.5 | 1.4, 1.6 | 2.5, 3.0 |
| Side-chain rms B (bond, angle) | 2.6, 3.0 | 2.8, 3.2 | 4.3, 5.1 |
Za: number of molecules in the asymmetric unit.
Rsym1 and Rsym2, Rsym for the overall data and last resolution shell, respectively.
Completeness: completeness for overall data and last resolution shell (parentheses, which is 2.1 to 2.0 Å for type 1 crystals and 3.0 to 2.8 Å for type 2 crystals, respectively).
R-value = Σhkl||Fo| − |Fc||/Σhkl|Fo|.
||A subset of the data (5%) was excluded from the refinement and used for the free R-value calculation.