Table 2.
Data collection and refinement statistics of wild type and point mutant GFAT-1.
| GFAT-1 WT +Glu+Glc6P +UDPGalNAc |
GFAT-1 G461E | GFAT-1 G461E +UDPGlcNAc |
GFAT-1 G451E | GFAT-1 G451E +UDP-GlcNAc |
|
|---|---|---|---|---|---|
| Wavelength (Å) | 1.00 | 0.97 | 0.97 | 1.00 | 1.00 |
| Resolution range (Å) |
49.15–2.48 (2.57–2.48) |
48.68–2.59 (2.68–2.59) |
48.21–2.72 (2.81–2.72) |
48.98–2.24 (2.32–2.24) |
48.73–2.42 (2.51–2.42) |
| Space group | P 41 21 2 | P 41 21 2 | P 41 21 2 | P 41 21 2 | P 41 21 2 |
| a, b, c (Å) | 152.0 152.0 165.8 | 152.8 152.8 166.0 | 152.5 152.5 164.9 | 154.1 154.1 162.9 | 153.2 153.2 162.5 |
| α, β, γ (°) | 90 90 90 | 90 90 90 | 90 90 90 | 90 90 90 | 90 90 90 |
| Total reflections | 601,542 (57,351) | 613,756 (59,726) | 464,957 (46,298) | 690,080 (646,13) | 992,398 (91,739) |
| Unique reflections | 68,982 (6701) | 61,581 (5916) | 52,752 (5146) | 93,589 (9028) | 74,011 (7226) |
| Multiplicity | 8.7 (8.6) | 10.0 (10.1) | 8.8 (9.0) | 7.4 (7.2) | 13.4 (12.7) |
| Completeness (%) | 99.8 (98.3) | 99.6 (97.2) | 99.7 (98.9) | 99.7 (97.5) | 99.9 (99.0) |
| Mean I/sigma (I) | 14.75 (1.15) | 17.49 (1.41) | 16.86 (1.44) | 16.87 (1.54) | 18.36 (1.54) |
| Wilson B-factor | 57.5 | 65.0 | 71.5 | 45.7 | 49.7 |
| Rmerge (%) | 11.0 (157.4) | 9.7 (144.5) | 10.0 (142.9) | 8.0 (109.8) | 12.9 (163.2) |
| Rmeas (%) | 11.7 (167.4) | 10.2 (152.2) | 10.6 (151.7) | 8.6 (118.3) | 13.4 (170.0) |
| Rpim (%) | 3.9 (56.1) | 3.2 (47.0) | 3.5 (50.2) | 3.2 (43.5) | 3.6 (47.4) |
| CC1/2 (%) | 99.9 (49.6) | 99.9 (54.1) | 99.9 (54.9) | 99.9 (62.7) | 99.9 (59.9) |
| CC* (%) | 100 (81.5) | 100 (83.8) | 100 (84.2) | 100 (87.8) | 100 (86.5) |
| Reflections used in refinement | 68,971 (6701) | 61,566 (5916) | 52,734 (5145) | 93,581 (9029) | 74,006 (7226) |
| Reflections used for R-free | 1935 (177) | 1967 (181) | 1940 (209) | 1976 (192) | 1991 (195) |
| Rwork (%) | 18.9 (29.3) | 19.2 (29.2) | 20.5 (30.6) | 18.8 (27.1) | 19.4 (27.9) |
| Rfree (%) | 22.2 (33.5) | 21.9 (31.1) | 23.4 (31.6) | 20.4 (31.8) | 22.3 (30.9) |
| CCwork (%) | 96.1 (71.8) | 96.2 (73.5) | 95.2 (70.1) | 96.5 (78.3) | 95.9 (77.8) |
| CCfree (%) | 94.5 (47.9) | 93.9 (66.5) | 93.6 (68.9) | 96.0 (70.9) | 94.9 (79.8) |
| Number of non-hydrogen atoms | 10,565 | 10,463 | 10,270 | 10,617 | 10,570 |
| Macromolecules | 10,390 | 10,367 | 10,228 | 10,454 | 10,332 |
| Ligands | 112 | 32 | 32 | 32 | 112 |
| Solvent | 63 | 64 | 10 | 131 | 126 |
| Protein residues | 1316 | 1310 | 1292 | 1320 | 1304 |
| RMS (bonds) (Å) | 0.003 | 0.002 | 0.002 | 0.003 | 0.002 |
| RMS (angles) (°) | 0.48 | 0.45 | 0.44 | 0.53 | 0.44 |
| Ramachandran favored (%) | 96 | 96 | 96 | 98 | 97 |
| Ramachandran allowed (%) | 3.8 | 3.7 | 4.1 | 2 | 2.4 |
| Ramachandran outliers (%) | 0.077 | 0.15 | 0 | 0.15 | 0.23 |
| Rotamer outliers (%) | 0.087 | 0.17 | 0.089 | 0.17 | 0.088 |
| Clashscore | 0.48 | 0.72 | 0.83 | 0.67 | 0.77 |
| Average B-factor | 87.35 | 109.55 | 115.46 | 70.93 | 78.97 |
| Macromolecules | 87.83 | 109.98 | 115.69 | 71.37 | 79.63 |
| Ligands | 64.10 | 78.68 | 62.07 | 44.41 | 54.72 |
| Solvent | 49.35 | 56.18 | 53.11 | 42.56 | 46.88 |
| Number of TLS groups | 4 | 4 | 4 | 4 | 4 |
| PDB code | 6SVM | 6R4I | 6SVQ | 6R4H | 6R4J |
Statistics for the highest-resolution shell are shown in parentheses