Table 1.
X-ray data collection and refinement statistics for data sets from a non-illuminated and an illuminated crystal of the D96A bacteriorhodopsin mutant. The illumination at 295K with red laser, as described in Methods, converted bacteriorhodopsin in the crystal to the M state with virtually full occupancy.
| Non-illuminated D96A |
Illuminated D96A |
Non-illuminated T46V |
|
|---|---|---|---|
| Data resolution range, Å | 2.0 – 25.0 | 2.08 – 25.0 | 1.84 – 25.0 |
| Total observations | 306,070 | 207,357 | 356,040 |
| Unique reflections | 15,618 | 13,966 | 19,393 |
| Rmerge a, b , % | 6.2 (75.6) | 6.6 (62.5) | 4.1 (53.7) |
| Average I/σ (I)b, c | 23.4 (2.9) | 23.4 (3.8) | 28.9 (2.1) |
| Completenessb, % | 99.9 (99.9) | 100.0 (100.0) | 95.5 (90.5) |
| Mosaicity, o | 0.57 | 0.61 | 0.84 |
| Refinement range, Å | 2.0 – 25.0 | 2.08 – 25.0 | 1.84 – 25.0 |
| Structure factors | 14,807 | 13,226 | 18,360 |
| Restraints | 8,206 | 8,240 | 8,223 |
| Parameters | 8,284 | 8,272 | 8,300 |
| Twin ratio | 97:3 | 58:42 | 99:1 |
| Protein atoms | 1717 | 1717 | 1720 |
| Retinal atoms | 20 | 20 | 20 |
| Water molecules | 23 | 23 | 24 |
| Lipid atoms | 310 | 310 | 310 |
| R-factord, e, % | 23.9 (19.8) | 15.6 (15.3) | 19.5 (17.2) |
| Rfree e, f, % | 29.9 (25.9) | 26.0 (23.7) | 26.0 (23.2) |
| Average protein B, Å2 | 32.0 | 29.2 | 30.9 |
| Average retinal B, Å2 | 25.0 | 22.7 | 20.5 |
| Average water B, Å2 | 38.3 | 39.5 | 34.0 |
| Average lipid B, Å2 | 68.5 | 71.1 | 72.6 |
| Deviation from ideal bond lengths, Å |
0.015 | 0.015 | 0.015 |
| Deviation from ideal bond angle distances, Å |
0.054 | 0.055 | 0.054 |
Rmerge (I) = Σhkl Σi | Ihkl,i − 〈Ihkl〉 | /Σhkl Σi | Ihkl,i | , where 〈Ihkl〉 is the average intensity of the multiple Ihkl,i observations for symmetry-related reflections.
I/σ(I), average of the diffraction intensities, divided by their standard deviations.
values in parentheses are for the 2.00 to 2.09 Å and the 2.08 to 2.17 Å shell resolution shells for the non-illuminated and the illuminated D96A crystal, respectively, and the 1.84 to 1.92 Å shell resolution shell for the T46V crystal.
R-factor = Σhkl | Fobs − Fcalc | / Σhkl | Fobs | , where Fobs and Fcalc are observed and calculated structure factors, respectively.
values are for all data, those in parentheses for F > 4σ(F).
Rfree = Σhkl ε T | Fobs − Fcalc | / Σhkl ε T | Fobs | , where a test set (5% of the data) is omitted from the refinement in such a way that all structure factors in each of several thin resolution-shells were selected to avoid bias from merohedral twinning.