Table 2. Data collection and crystallographic refinement statistics for mutant P2O structures with fluorinated galactoses.
| Data collection1 | ||||||||
| Protein variant | H167A3Fgal | H167A2Fgal | H450G3Fgal | H450G2Fgal | V546C3Fgal | V546C2Fgal | H450G/V546C3Fgal | H450G/V546C2Fgal |
| Cell constants a, b, c (Å); β (°) | 99.875, 102.295, 136.957; 90.78 | 100.291, 102.476, 137.423; 91.02 | 99.896, 102.423, 137.365; 91.19 | 101.672, 101.672, 127.562 | 99.971, 102.980, 137.654; 90.92 | 101.724, 101.724, 251.284 | 100.242, 102.469, 137.840; 91.09 | 102.423, 102.423, 119.033 |
| Space group/molecules per a.s.u. | P21/4 | P21/4 | P21/4 | P42212/1 | P21/4 | P43212/2 | P21/4 | P42212/1 |
| Beamline, λ (Å) | Diamond, I24,0.9191 | Diamond, I24,0.9191 | MAX II, I911-3,1.0000 | MAX II, I911-3,1.0000 | Diamond, I24,0.9191 | SLS PX1 (X06SA),1.0000 | PETRA III, P13,0.9465 | Diamond, I24,0.9191 |
| Resolution range, all (Å) | 47.92–1.90 | 48.01–2.00 | 57.14–1.90 | 54.03–1.65 | 48.23–2.30 | 47.32–1.60 | 49.33–1.50 | 47.04–1.80 |
| Resolution range, outer shell (Å) | 2.00–1.90 | 2.10–2.00 | 2.00–1.90 | 1.70–1.65 | 2.40–2.30 | 1.70–1.60 | 1.60–1.50 | 1.90–1.80 |
| Unique reflections | 216,233 (30,699) | 184,127 (24,662) | 215,840 (30,624) | 80,572 (6,649) | 123,398 (14,694) | 173,572 (28,468) | 442,699 (77,654) | 59,195 (8,727) |
| Multiplicity | 6.7 (6.8) | 6.9 (7.0) | 3.7 (3.7) | 12.9 (9.0) | 6.1 (6.2) | 25.3 (25.6) | 7.4 (7.3) | 26.1 (27.1) |
| Completeness (%) | 99.8 (99.8) | 98.2 (97.2) | 99.2 (99.1) | 99.7 (97.6) | 99.5 (99.6) | 100 (100) | 99.7 (99.7) | 100 (100) |
| <I/σI> | 13.2 (2.1) | 11.5 (2.4) | 10.3 (2.6) | 27.1 (3.8) | 8.7 (1.6) | 14.1 (2.2) | 11.9 (1.6) | 15.4 (2.1) |
| Rsym 2 (%) | 10.8 (102.0) | 17.6 (93.8) | 20.6 (88.7) | 7.4 (71.3) | 17.2 (129.3) | 23.1 (164.7) | 9.2 (125.3) | 26.0 (236.4) |
| CC(1/2)3 | 99.8 (75.1) | 99.4 (75.8) | 98.3 (73.5) | 99.9 (81.7) | 99.4 (65.8) | 99.8 (73.4) | 99.9 (59.0) | 99.8 (75.1) |
| Crystallographic refinement | ||||||||
| Resolution range, all (Å) | 47.92–1.90 | 48.01–2.00 | 50–1.90 | 50.0–1.65 | 48.23–2.30 | 47.32–1.60 | 49.33–1.50 | 47.04–1.80 |
| Resolution range, outer shell (Å) | 2.00–1.90 | 2.11–2.00 | 2.00–1.90 | 1.74–1.65 | 2.36–2.30 | 1.69–1.60 | 1.58–1.50 | 1.90–1.80 |
| Completeness, all % (outer bin) | 99.8 (99.8) | 98.2 (97.1) | 99.2 (99.1) | 99.8 (98.5) | 99.5 (99.6) | 100 (100) | 99.7 (99.7) | 100 (100) |
| Rfactor 4/work reflns, all | 0.170/215,167 | 0.186/182,281 | 0.239/211,9755 | 0.192/78,664 | 0.194/122,372 | 0.182/171,834 | 0.156/441,592 | 0.162/58,172 |
| Rfree/free reflns, all | 0.214/1,066 | 0.222/1,846 | 0.280/3,8655 | 0.224/1,907 | 0.248/984 | 0.212/1,737 | 0.198/1,107 | 0.199/1,022 |
| Number of amino-acid residues | 2,297 | 2,295 | 2,300 | 576 | 2,300 | 1,139 | 2,301 | 576 |
| Non-hydrogen atoms | 20,179 | 20,233 | 19,522 | 5,115 | 19,647 | 10,344 | 21,660 | 5,035 |
| Mean B (Å2) protein all/mc/sc | 32.5/31.1/33.9 | 34.4/32.8/36.1 | 24.7/23.6/25.9 | 17.6/16.7/18.6 | 29.6/38.6/40.6 | 17.6/16.3/19.0 | 24.4/22.9/25.9 | 22.4/21.0/23.8 |
| Mean B (Å2) solvent/No. mol. | 35.5/1,793 | 40.2/1,766 | 26.1/1,067 | 25.3/514 | 34.2/1,174 | 26.0/1,135 | 35.5/3,062 | 30.1/405 |
| Rmsd bond lengths (Å), angles (°) | 0.019, 1.90 | 0.019, 1.92 | 0.018, 1.96 | 0.021, 2.11 | 0.015, 1.76 | 0.023, 2.16 | 0.027, 2.28 | 0.020, 2.06 |
| Ramachandran6: favored (%)/allowed (%)/Outliers | 97.0/99.9/2 | 97.2/100/0 | 96.9/100/1 | 97.4/100/0 | 97.1/100/1 | 97.8/100/0 | 97.8/100/0 | 97.9/100/0 |
| PDB accession code | 4MOK | 4MOL | 4MOM | 4MOO | 4MOP | 4MOQ | 4MOR | 4MOS |
The outer shell statistics of the reflections are given in parentheses. Shells were selected as defined in XDS [36] by the user.
Rsym = [Σhkl Σi |I–<I>|/Σhkl Σi |I| ]×100%.
CC(1/2) = Percentage of correlation between intensities from random half-datasets. Values given represent correlations significant at the 0.1% level [44].
Rfactor = Σhkl | |Fo|–|Fc| |/Σhkl |Fo|.
We note that the R and Rfree values are suspiciously high a 1.9-Å resolution model with electron density of good quality. Data sanity tests excluded twinning, pseudotranslation, and misindexing as possible reasons. However, the data suffer from poor completeness in the low-resolution region and contain several ice rings, which may account for the problems encountered during refinement.
As determined by MolProbity [45].