Table 1. Crystallization, data collection, and refinement statistics summary for mFAHD1 crystals and structure models.
| Crystallization and data collection | ||
| Protein | mFAHD1, native | mFAHD1–oxalate complex |
| Model (PDB identifiers) | Chains A, B, C, D in 6SBJ | Chain A, B, C, D in 6SBI |
| Protein stock solution | 1.5–2.0 μg/μl, SEC quality | |
| Crystallization conditions | 25% (w/v) PEG 3350, 0.2 M MgCl2 and 0.1 M Bis/Tris pH 5.5 | 20% (w/v) PEG 4000, 0.05 M MgCl2 and 0.1 M MES pH 5.5, 1mM Na-oxalate |
| Beam line, wavelength (Å) | ESRF MASSIF-1, 0.96598 | |
| ESRF data identification link* | https://doi.esrf.fr/10.15151/ESRF-DC-186917546 | https://doi.esrf.fr/10.15151/ESRF-DC-187128349 |
| Crystal volume (mm3) | 10−6 to 10−5 | |
| Space group (number) | P21 (4) | |
| Cell parameters (Å) Cell parameters (°) |
52.40, 69.96, 107.56 90.0, 92.25, 90.0 |
52.60, 103.35, 86.60 90.0, 90.21, 90.0 |
| Unit cell volume (Å3) | 393781 | 470545 |
| Solvent fraction, VM (Å3/Da) | 0.27, 1.68 | 0.39, 2.00 |
| Wilson B-factor (Å2) | 35.6 | 38 |
| Resolution1 (Å) anisotropic (Å) |
42.65-2.22 (2.47-2.22) 2.22, 2.37, 2.77 |
44.38-2.70 (2.97-2.70) 2.81, 3.93, 2.65 |
| Completeness1, spherical elliptic (%) |
64.2 (12.5) 85.3 (43.2) |
62.2 (12.2) 91.2 (51.4) |
| Observed reflections1 | 89978 (4432) | 54166 (2621) |
| Unique reflections1 | 26144 (1316) | 15791 (790) |
| Average redundancy1 | 3.44 (3.38) | 3.43 (3.32) |
| < I/σ(I)>1 | 4.6 (1.4) | 4.2 (1.4) |
| Rmeas1,2 | 0.30 (1.14) | 0.20 (0.65) |
| Rmerge1,3 | 0.25 (0.96) | 0.17 (0.54) |
| CC1/21,4 | 0.963 (0.553) | 0.985 (0.756) |
| Refinement | ||
| Resolution, refinement1(Å) | 42.65-2.2 (2.27-2.22) | 44.37-2.70 (2.77-2.70) |
| Rfree (5% set), Rwork1 | 0.257 (0.345), 0.193 (0.265) | 0.234 (0.508), 0.187 (0.290) |
| Coordinate errors (free DPI, σA), (Å) | 0.341, 0.231 | 0.505, 0.372 |
| Fo vs. Fc correlation, free | 0.926, 0.876 | 0.923, 0.887 |
| All refined non-H, n, <B> (Å2) | 6871 (34.7) | 6785 (32.0) |
| TLS groups | 4 (1 for each molecule) | |
| OXL ligands | 0 | 4 (1 per molecule) |
| Mg2+ cations | 6 (1 per molecule + 2 intermolecular) | 4 (1 per molecule) |
| K+ cations | 0 | 2 |
| Cl− anions | 6 | 9 |
| Water molecules | 120 | 35 |
| Geometry | ||
| r.m.s.d. bond lengths, angles (Å, °) | 0.007, 1.47 | 0.007, 1.50 |
| Ramachandran preferred, allowed, outliers5 | 789 (96%), 30 (4%), 0 (0%) | 813 (95%), 42 (45%), 0 (0%) |
*
Image prefixes are: mesh, mesh scan images; line, the line scan images; ref, four characterization images (90 deg apart); the actual dataset image has no prefix.
1Values in parentheses are for the highest resolution shell.
2,3As defined in (International Union of Crystallography, 2012) [28].
4CC1/2 is Pearson’s correlation coefficient between two randomly assigned datasets each derived by averaging half of the observations for a given reflection as defined in (Karplus and Diederichs, 2012) [29].
5Determined using the Ramachandran plot boundaries defined in Molprobity (Chen et al., 2010) [30].