Extended Data Table 1.
Data collection, phasing and refinement statistics. Data collection statistics are from HKL300032; phasing statistics are from SHARP33; refinement statistics are from PHENIX36. CC1/2 is defined in40; Clash Score is defined in38. Rsym = Σ | Ii - < Ii > | / Σ Ii, where < Ii > is the average intensity of symmetry-equivalent reflections. 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. R-factor = Σ | Fo – Fc | / Σ | Fo |, where Fo and Fc are the observed and calculated structure factors, respectively. Rfree = R-factor calculated using a subset (~ 5%) of reflection data chosen randomly and omitted throughout refinement. Numbers in parentheses indicate the highest resolution shells and their statistics.
| ICMT-monobody Native |
ICMT-monobody SeMet |
ICMT Native |
|
|---|---|---|---|
| Data Collection | APS 24-ID-C | APS 23-ID-D | APS 23-ID-D |
| Space group | P212121 | P212121 | C2221 |
| Wavelength (Å) | 0.9790 | 0.9791 | 1.0332 |
| Cell dimensions: | |||
| a, b, c (Å) | 40.6, 87.7, 147.7 | 40.8, 88.7, 148.4 | 51.6, 123.6, 236.1 |
| α, β, γ (°) | 90, 90, 90 | 90, 90, 90 | 90, 90, 90 |
| Resolution (Å) | 31 – 2.3 (2.34 – 2.3) | 40 – 3.0 (3.05 – 3.0) | 33 – 4.0 (4.07 – 4.0) |
| No. of crystals | 1 | 9 | 1 |
| Rmerge (%) | 20.6 (97.9) | 64.2 (>100.0) | 7.1 (>100.0) |
| Rsim (%) | 6.2 (29.5) | 9.6 (57.0) | 1.2 (34.0) |
| I/σI | 13.3 (2.5) | 15.5 (2.0) | 85 (3.0) |
| Completeness (%) | 97.2 (99.8) | 100.0 (100.0) | 100.0 (100.0) |
| Redundancy | 11.2 (11.1) | 45.7 (47.9) | 34.6 (35.6) |
| SIRAS Phasing | 30 – 4.0 Å | ||
| No. of sites | 5 | ||
| Phasing Power (iso / ano) | 0.129/0.292 | ||
| Rcullis (iso / ano) (%) | 95.5/97.5 | ||
| Figure of Merit (acentric / centric) | 0.183/0.047 | ||
| Refinement | |||
| Resolution (Å) | 31 – 2.3 (2.4 – 2.3) | 33 – 4.0 (5.0 – 4.0) | |
| No. of reflections | 23,203 | 6,119 | |
| Rwork (%) | 21.4 (26.9) | 36.9 (45.0) | |
| Rfree (%) | 24.6 (32.2) | 38.9 (42.2) | |
| No. atoms | |||
| Protein | 3039 | 2250 | |
| Ligands | 319 | 26 | |
| Water | 92 | ||
| Average B-factors (Å2) | |||
| Protein | 33.4 | 209.6 | |
| Ligands | 58.6 | 200.7 | |
| Water | 38.7 | ||
| Ramachandran (%) | |||
| Favoured | 98.1 | 97.3 | |
| Outliers | 0.0 | 0.0 | |
| R.m.s. deviations | |||
| Bond lengths (Å) | 0.003 | 0.004 | |
| Bond angles (°) | 0.595 | 0.745 | |
| Clash Score | 2.3 | 24 |