Table 1. Statistics of the structure analysis.
| Data set
|
|||||
|---|---|---|---|---|---|
| apo-PhAlaXD-HIS
|
|||||
| Parameter | Peak | Edge | Remote | PhAlaXD-HIS-Ser-Zn2+ | WT-PhAlaXM-Zn2+ |
| Data collection statistics* | 0.9797 | 0.9800 | 0.9000 | 1.0000 | 0.9793 |
| Wavelength, Å | SPring-8 BL38B1 | PF BL6A | SPring-8 BL41XU | ||
| X-ray source | P212121 | P212121 | P21 | ||
| Unit cell, Å | 34.2, 88.7, 110.1 | 34.0, 88.5, 109.9 | 42.5, 98.0, 60.6, β = 95.8° | ||
| Unique reflections | 10,320 | 10,576 | 9,907 | 8,871 | 39,904 |
| Resolution, Å | 50.0-2.64 | 50.0-2.62 | 50.0-2.68 | 50.0-2.80 | 50.0-1.88 |
| Completeness, % | 99.7 (99.8) | 99.7 (99.6) | 99.7 (99.9) | 100.0 (100.0) | 99.8 (98.8) |
| Redundancy | 6.4 (6.0) | 6.3 (5.8) | 6.4 (5.9) | 8.8 (8.6) | 5.5 (4.7) |
| Rmerge,† % | 9.0 (39.1) | 8.1 (39.4) | 8.4 (39.6) | 9.3 (40.5) | 7.1 (38.2) |
| Refinement statistics | |||||
| Resolution, Å | 15.0-2.62 | 15.0-2.80 | 50.0-1.88 | ||
| Number of atoms (Protein/water/l-serine/zinc) | 2,514/107/0/0 | 2,497/107/14/2 | 3,737/422/0/3 | ||
| R factor‡/Rfree,§ % | 23.5/27.3 | 22.7/26.6 | 19.3/23.2 | ||
| rmsd bond lengths, Å/bond angles, ° | 0.011/1.4 | 0.0084/1.3 | 0.0050/1.3 | ||
| Ramachandran plot, % (favored/allowed/generous/disallowed) | 84.4/15.3/0.4/0 | 90.9/9.1/0/0 | 93.9/6.1/0/0 | ||
| Average B factor, Å2 | 51.8 | 41.0 | 26.7 | ||
rmsd, rms deviation.
*
Values in parentheses are for the highest resolution shell.
†
Rmerge = {ΣhΣi |〈I(h)〉 - I(h)i|}/ΣhΣi |I(h)i, where I(h)i is the ith observation of reflection h and 〈I(h)〉 is the mean intensity of all observations of reflection h.
‡
R factor = {Σ∥Fobs|-|Fcalc∥} |Σ|Fobs|, where Fobs and Fcalc are observed and calculated structure factor amplitudes.
§
Rfree was calculated for 6.5%, 7.0%, and 10% randomly selected reflections of free, ser-Zn2+, and Zn2+ complex data sets that were not used in the refinement.