Table 1. H206A Oraicryst data collection, phasing and refinement statistics.
Data collection statistics are from HKL3000 (Otwinowski and Minor, 1997) or XDS (I- experiment) (Kabsch, 2010). Rsym = Σ | Ii- < Ii > | / Σ Ii, where < Ii > is the average intensity of symmetry-equivalent reflections. CC1/2, CCwork and CCfree are defined in (Karplus and Diederichs, 2012). Phasing power = RMS (|F|/ε), where |F| is the heavy-atom structure factor amplitude and ε is the residual lack of closure error. Rcullis is the mean residual lack of closure error divided by the dispersive or anomalous difference. Rwork = Σ | Fobs – Fcalc | / Σ | Fobs |, where Fobs and Fcalc are the observed and calculated structure factors, respectively. Rfree is calculated using a subset (~10%) of reflection data chosen randomly and omitted throughout refinement. Figure of merit is indicated after density modification and phase extension starting from 9.0 Å in DM. R.m.s.d: root mean square deviations from ideal geometry. Numbers in parentheses indicate the highest resolution shells and their statistics.
| H206A Oraicryst | ||||
|---|---|---|---|---|
| Native | Ba2+ | Gd3+ | I- | |
| Space group | I41 | I41 | I41 | I41 |
| Datasets source | APS 24ID-C | APS 24ID-C | APS 23ID-D | APS 23ID-D |
| Wavelength (Å) | 1.1000 | 1.7000 | 1.7000 | 1.7085 |
| Cell dimensions: | ||||
| a, b, c (Å) | 262.3, 262.3, 220.4 | 265.0, 265.0, 219.9 | 255.4, 255.4, 216.0 | 266.4, 266.4, 221.5 |
| α= β= γ (°) | 90 | 90 | 90 | 90 |
| Resolution (Å) | 50–6.70 (6.82–6.70) | 50–7.40 (7.53–7.40) | 50–7.90 (8.04–7.90) | 50–7.6 (7.68–7.60) |
| No. of crystals | 1 | 1 | 1 | 2 |
| Rsym (%) | 8.3 (>100) | 22.5 (>100) | 12.1 (>100) | 14.0 (>100) |
| Rpim (%) | 1.1 (57.0) | 3.4 (46.7) | 2.4 (42.8) | 1.1 (62.0) |
| CC1/2 (in outer shell) | 0.214 | 0.173 | 0.158 | 0.493 |
| I/σI | 92.4 (1.1) | 47.0 (1.4) | 37.5 (2.0) | 26.8 (0.2) |
| Completeness (%) | 100.0 (100.0) | 100.0 (100.0) | 100.0 (100.0) | 99.9 (99.7) |
| Redundancy | 55.8 (58.7) | 46.5 (51.8) | 25.1 (26.0) | 165.1 (172.5) |
| Figure of Merit (DM) | 0.729 [20–6.7 Å] | |||
| Refinement | PDB ID: 6BBF | |||
| Resolution (Å) | 20–6.7 | |||
| No. of reflections | 12844 | |||
| Rwork (%) | 30.6 | |||
| Rfree (%) | 33.9 | |||
| CCwork/CCfree (in outer shell) | 0.285/0.220 | |||
| No. atoms | 27120 | |||
| Ramachandran (%) | ||||
| Favored | 97.22 | |||
| Outliers | 1.04 | |||
| R.m.s.d: | ||||
| bond lengths (Å) | 0.005 | |||
| bond angles (°) | 1.15 | |||