Table 1.
Data collection and refinement statistics
| Crystal | ||||
| Ephexin4DPSH (SeMet) | Ephexin4DPSH (Native) | Ephexin4IDPSH | ||
| Data collection and processing | ||||
| Source | SSRF-BL19U1 | SSRF-BL19U1 | SSRF-BL18U1 | |
| Wavelength, Å | 0.97775 | 0.97775 | 0.97915 | |
| Space group | P3112 | P3112 | P65 | |
| Unit cell (a,b,c), Å | 144.5, 144.5, 290.7 | 144.4, 144.4, 290.5 | 143.1, 143.1, 138.5 | |
| Unit cell (α,β,γ), ° | 90, 90, 120 | 90, 90, 120 | 90, 90, 120 | |
| Resolution range, Å | 50–2.59 (2.75–2.59) | 50.00–2.39 (2.48–2.39) | 50.00–3.00 (3.11–3.00) | |
| No. of unique reflections | 108,283 (20,188) | 136,390 (13,383) | 31,720 (3,161) | |
| Redundancy | 20.1 (20.7) | 13.7 (13.7) | 7.0 (6.6) | |
| I/σ(I) | 9.0 (2.4) | 9.7 (2.7) | 14.2 (1.5) | |
| Completeness, % | 99.6 (97.5) | 99.8 (98.4) | 96.5(90.2) | |
| Rmerge, %* | 18.2 (85.6) | 18.8 (85.4) | 8.9 (95.5) | |
| CC1/2 | 99.1 (85.9) | 99.2 (88.7) | 99.8 (53.9) | |
| Wilson B | 46.0 | 43.5 | 82.6 | |
| Phase determination | ||||
| Anomalous scatterer | Selenium (23 of 28 possible sites) | |||
| Mean FOM | 0.3027 | |||
| Structure refinement | ||||
| Resolution, Å | 48.42–2.39 | 46.83–3.00 | ||
| Rcryst†/Rfree‡, % | 17.95/20.24 | 18.50/23.10 | ||
| rmsd bonds, Å/angles, ° | 0.009/1.150 | 0.013/1.660 | ||
| No. of protein atoms | 13,980 | 7,349 | ||
| No. of solvent atoms | 613 | 0 | ||
| Average B factor, Å2 | 53.7 | 88.3 | ||
| Ramachandran plot, % | ||||
| Most favored regions | 98.2 | 97.8 | ||
| Additionally allowed | 1.8 | 2.2 | ||
| Generously allowed | 0 | 0 | ||
Numbers in parentheses represent the value for the highest resolution shell. FOM, figures of merit; rmsd, root-mean-square deviation.
*
Rmerge = ∑|Ii − Im|/∑Ii, where Ii is the intensity of the measured reflection, and Im is the mean intensity of all symmetry related reflections.
†
Rcryst = Σ||Fobs| − |Fcalc||/Σ|Fobs|, where Fobs and Fcalc are observed and calculated structure factors.
‡
Rfree = ΣT||Fobs| − |Fcalc||/ΣT|Fobs|, where T is a test dataset of about 5% of the total reflections randomly chosen and set aside prior to refinement.