Extended Data Table 1. Data collection, phasing and refinement statistics.
| Native, pH 7 5F0Ya | PCMBSb | Gdc | VILd | Native, pH 10 5F0Ze | Native, pH 5 5G37f | |
|---|---|---|---|---|---|---|
| Data collection | ||||||
| Space group | P212121 | P212121 | P212121 | P212121 | P212121 | P212121 |
| Cell dimensions | ||||||
| a, b, c (Å) | 86.9, 97.4, 128.3 | 87.1, 97.8, 128.4 | 87.0, 97.5, 128.1 | 86.7, 97.3, 127.7 | 86.7, 97.3, 127.7 | 86.8, 97.0, 127.0 |
| α, β, γ (°) | 90, 90, 90 | 90, 90, 90 | 90, 90, 90 | 90, 90, 90 | 90, 90, 90 | 90, 90, 90 |
| Wavelength (Å) | 1.212 | 1.408 | 1.408 | 1.408 | 1.459 | 1.459 |
| X-ray beam focus (μm) | 1.3 | 1.3 | 1.3 | 1.3 | 0.25 | 0.25 |
| Photons/pulse (× 1011) | 1.9 | 7.2 | 7.2 | 7.2 | 6.4 | 6.4 |
| Pulse duration (fs) | 31.9 | 45.1 | 45.1 | 45.1 | 40.8 | 40.8 |
| Absorbed dose (GGy)g | 0.03 | 0.15 | 0.15 | 0.15 | 14.4 | 14.4 |
| Number of collected frames | 312,659 | 761,052 | 431,986 | 264,770 | 371,386 | 493,979 |
| Number of indexed patterns | 41,206 | 184,091 | 131,137 | 42,537 | 27,792 | 17099 |
| Number of indexed images accepted by cctbx.prime | 40,794 | 170,616 | 123,484 | 39,789 | 26,022 | 16224 |
| Resolution (Å)h | 43.5-2.25 (2.29-2.25) | 43.5-2.40 (2.44-2.40) | 43.5-2.35 (2.39-2.35) | 43.5-2.60 (2.64-2.60) | 43.5-2.37 (2.44-2.37) | 43.5-2.50 (2.54-2.50) |
| Number of observationsi | 12,854,588 | 53,361,546 | 39,314,393 | 11,249,082 | 12,069,895 | 5,495,157 |
| I/σI | 2.4 (0.5) | 2.8 (0.7) | 3.1 (0.6) | 3.7 (0.9) | 2.7 (0.9) | 6.34 (2.46) |
| CCl/2 | 96.8 (26.2) | 98.6 (16.2) | 98.4 (3.5) | 96.3 (17.5) | 97.3 (34.1) | 86.8 (28.0) |
| Completeness (%) | 99.7 (99.7) | 99.8 (96.9) | 99.8 (97.0) | 99.4 (96.2) | 99.9 (100.0) | 99.9 (89.4) |
| Multiplicity | 65.9 (4.8) | 372 (4.3) | 260.1 (4.4) | 100.4 (4.7) | 88.8 (19.2) | 76.62 (8.61) |
| Refinement | ||||||
| Refinement target function | Phased maximum-likelihood | Maximum-likelihood | Maximum-likelihood | |||
| Resolution (Å) | 2.25 (2.30 – 2.25) | 2.40 (2.46 – 2.40) | 2.50 (2.56 – 2.50) | |||
| Number of reflections | 52379 (3523) | 42817 (2923) | 37785(2557) | |||
| Rwork / Rfreeg | 0.164(0.288)/ 0.200 (0.327) | 0.165 (0.264)/ 0.211(0.311) | 0.211(0.357)/ 0.262 (0.427) | |||
| Number of atoms | ||||||
| Protein | 6479 | 6350 | 6415 | |||
| Water | 571 | 730 | 720 | |||
| B-factors (Å2) | ||||||
| Protein (BinA/BinB) | 47.5 / 40.7 | 52.8 / 47.3 | 39.2/36.8 | |||
| Water | 50.8 | 62.4 | 41.01 | |||
| R.m.s. deviations | ||||||
| Bond lengths (Å) | 0.006 | 0.007 | 0.002 | |||
| Bond angles (°) | 1.359 | 0.8 | 0.5 |
41,206 crystals were used to produce the native, pH 7 dataset.
184,091 crystals were used to produce the PCMBS dataset.
131,137 crystals were used to produce the Gd dataset.
42,537 crystals were used to produce the VIL dataset.
27,792 crystals were used to produce the native, pH 10 dataset.
17099 crystals where used to produce the native, pH 5 dataset.
As calculated by Raddose-3D70. Note that these dose calculations do not yet take into account the escape of photoelectrons from the diffracting volume. The track length in protein and water of photoelectrons has been estimated to 3 μm, for 1 Å wavelength X-rays71, suggesting that most photoelectrons travel outside of the diffracting volume without losing all their energy within it (crystals are 0.25 * 0.35 * 0.75 μm3 on average). Although these are not the only electrons to contribute to the damage, a preliminary photoelectron escape model incorporated into an unreleased version of RADDOSE-3D suggests that the absorbed dose is overestimated by a factor of ∼100 (J. Brooks-Bartlett and E. Garman, personal communication) for these small crystals.
Values in parentheses are for highest-resolution shell.
Including negative intensity observations.