Table 1.
Statistics of crystal data collection and refinement for native (AGDC1 and PPP2) and selenium-methionine derivatized proteins (PPP2-Se).
| Data | AGDC1 | AGDC1-APO | PPP2 | PPP2-Se |
|---|---|---|---|---|
| PDB ID | 6W54 | 7KD9 | 7JMV | 7JMR |
| Resolution range (Å) | 50–1.50 | 50–1.94 | 50–1.57 | 50–1.67 |
| Space group | R 3 | P 21 21 2 | P 3 2 1 | P 3 2 1 |
| Unit cell (Å) | 81.97, 81.97, 103.1 | 91.63, 265.3, 93.73 | 98.74, 98.74, 62.29 | 98.85, 98.85, 62.38 |
| Unit cell (deg) | 90, 90, 120 | 90, 90, 90 | 90, 90, 120 | 90, 90, 120 |
| Wavelength (Å) | 1.23984 | 1.0 | 0.97934 | 0.97934 |
| Beam lines | GM/CA-CAT, APS | GM/CA-CAT, APS | GM/CA-CAT, APS | GM/CA-CAT, APS |
| Number of measurements | 148,680 | 827,460 | 481,052 | 675,504 |
| Number of unique reflections | 36,568 | 168,891 | 49,087 | 40,823 |
| Completeness of data (%) | ||||
| Overall | 88.5 | 99.5 | 99.9 | 99.6 |
| Shell/resolution range (Å) | 40.2 (1.53–1.50) | 96.8 (2.00–1.94) | 99.5 (1.60–1.57) | 98.8 (1.73–1.67) |
| 99.2 (50–1.69) | ||||
| Rsym (%) | ||||
| Overall | 9.4 | 9.0 | 8.0 | 7.0 |
| Last shell/resolution range (Å) | 35.7 (1.53–1.50) | 90.2 (2.00–1.94) | 89.4 (1.60–1.57) | 70.3 (1.73–1.67) |
| CC1/2 | ||||
| Last shell/resolution range (Å) | 0.819 (1.53–1.50) | 0.695 (2.00–1.94) | 0.795 (1.60–1.57) | 0.762 (1.73–1.67) |
| I/sigma | ||||
| Overall | 42.9 | 15.2 | 41.4 | 38.9 |
| Last shell/resolution range (Å) | 5.8 (1.53–1.50) | 1.4 (2.00–1.94) | 1.8 (1.60–1.57) | 1.6 (1.73–1.67) |
| Wilson B-factor | 18.29 | 33.46 | 20.35 | 27.8 |
| SAD—figure of merit (%) | 52.0 | |||
| Rwork | 14.03 | 19.10 | 18.17 | 17.77 |
| Rfree | 16.62 | 23.75 | 19.34 | 20.12 |
| Number of atoms | 2057 | 17,583 | 1942 | 1979 |
| Macromolecules | 1845 | 16,819 | 1805 | 1813 |
| Ligands | 13 | 3 | 14 | 4 |
| Solvent | 199 | 761 | 123 | 162 |
| Mean B (Å2) | 25.0 | 50.28 | 24.1 | 32.8 |
| RMS (bonds) | 0.008 | 0.007 | 0.010 | 0.010 |
| RMS (angles) | 0.97 | 0.91 | 1.04 | 1.06 |
| Ramachandran favored (%) | 97.72 | 95.72 | 97.26 | 96.82 |
| Ramachandran allowed (%) | 2.28 | 4.23 | 2.74 | 3.18 |
| Ramachandran outliers (%) | 0 | 0.05 | 0 | 0 |
| Rotamer outliers (%) | 0 | 0 | 0 | 0 |
Rsym = Σj Σi |Iij—< Ij >| / Σi Σj Iij, where i runs over multiple obervations of the same intensity, and j runs over all crystallographic unique intensities. Rfactor = Σ ||Fobs|—|Fcalc|| /Σ |Fobs|. Rfree was calculated with 5% of the reflections selected.