Table 1.
Crystallographic data and model refinement. Values in parentheses are for the highest resolution shell.
| PDB ID: | 5BW6 | 4Y6G | 4WX2 | 4ZQC |
|---|---|---|---|---|
| X-ray source | MicroMax-007HF | MicroMax-007HF | MicroMax-007HF | ALS-SIBYLS |
| Wavelength (Å) | 1.5418 | 1.5418 | 1.5418 | 0.9793 |
| C 1 2 1 (No. 5) | C 1 2 1 (No. 5) | C 1 2 1 (No. 5) | C 1 2 1 (No. 5) | C 1 2 1 (No. 5) |
| Unit-cell parameters | ||||
| a, b, c (Å) | 183.03, 58.90, 67.23 | 184.17, 59.84, 67.30 | 183.81, 58.89, 67.27 | 183.53, 58.63, 67.22 |
| α, β, γ (°) | 90.00, 94.91, 90.00 | 90.00, 94.91, 90.00 | 90.00, 95.21, 90.00 | 90.00, 94.92, 90.00 |
| Rotation (Å) | 122 | 160 | 175 | 200 |
| No. of images | 244 | 320 | 350 | 200 |
| Resolution range (Å) | 20.00–1.82 (1.92–1.82) | 21.69–1.65 (1.74–1.65) | 20.95–1.75 (1.84–1.75) | 30.00–1.54 (1.62–1.54) |
| No. of reflections | 100061 (13824) | 276270 (37626) | 250959 (35470) | 376716 (53926) |
| No. of unique reflections | 46573 (6445) | 87302 (12471) | 72402 (10537) | 99870 (14139) |
| Rmerge † (%) | 4.3 (45.4) | 4.6 (45.8) | 6.9 (46.1) | 10.5 (55.6) |
| Completeness (%) | 72.8 (69.7) | 99.4 (98.0) | 99.9 (100.0) | 95.0 (92.4) |
| Redundancy | 2.1 (2.1) | 3.2 (3.0) | 3.5 (3.4) | 3.8 (3.8) |
| Mean I/σ(I) | 13.1 (2.00) | 11.9 (2.3) | 9.9 (2.10) | 7.2 (2.1) |
| CC1/2 ╪ (%) | 99.9 (75.6) | 99.9 (85.0) | 99.8 (89.9) | 98.7 (81.3) |
| Mosaicity (°) | 1.68 | 0.63 | 0.81 | 0.64 |
| Refinement statistics | ||||
| Resolution (Å) | 19.83–1.82 | 21.69–1.65 | 20.95–1.75 | 29.31–1.54 |
| Total of reflections | 44334 | 82910 | 72402 | 94912 |
| Rwork/Rfree ¥ (%) | 16.82/21.43 | 15.82/17.91 | 15.84/18.85 | 13.57/18.66 |
| No. of non-H atoms | ||||
| Protein | 4924 | 4943 | 4905 | 5018 |
| PLP | 15 | 15 | 15 | 15 |
| F6F | 21 | 42 | 63 | 63 |
| EDO | - | - | 4 | - |
| PEG | - | - | 7 | - |
| Na | 1 | 1 | 1 | 1 |
| DMSO | - | - | - | 48 |
| Water | 650 | 732 | 604 | 831 |
| Average B-factors (Å2) | ||||
| Protein | 24.57 | 25.90 | 25.97 | 17.84 |
| PLP | 14.09 | 16.62 | 18.20 | 11.29 |
| F6F | 39.18 | 33.77 | 34.35 | 21.16 |
| EDO | - | - | 53.59 | - |
| PEG | - | - | 40.82 | - |
| Na | 12.55 | 16.85 | 14.62 | 12.33 |
| DMSO | - | - | - | 30.15 |
| Water | 35.23 | 38.36 | 35.62 | 34.89 |
| R.m.s. deviations from ideality | ||||
| Bond lengths (Å) | 0.014 | 0.020 | 0.016 | 0.016 |
| Bond angles (°) | 1.659 | 1.951 | 1.720 | 1.736 |
| Ramachandran plot ‡ | ||||
| Most favored regions | 516 (93.8%) | 521 (94.2%) | 514 (93.8%) | 529 (94.1%) |
| Allowed regions | 33 (6.0%) | 31 (5.6%) | 33 (6.0%) | 32 (5.7%) |
| Generously allowed regions | 1 (0.20%) | 1 (0.20%) | 1 (0.20%) | 0 (0%) |
| Disallowed | 0 (0%) | 0 (0%) | 0 (0%) | 1 (0.20%) |
†
Rmerge = Σhkl Σi |Ii(hkl) − <I(hkl)>| / Σhkl Σi Ii(hkl), where Ii(hkl) and <I(hkl)> are the observed individual and mean intensities of a reflection with the indices hkl, respectively, Σi is the sum over i measurements of a reflection with the indices hkl, and Σhkl is the sum over all reflections.
╪
CC1/2 indicates the percentage of correlation between intensities of random half data sets.[73]
¥
R = Σhkl ||Fobs| − |Fcalc|| / Σhkl|Fobs|. Rfree is the R value calculated for a random 5% of the data set not included in the refinement.
‡
Percentage of residues in Ramachandran plot regions were determined using PROCHECK.[56]