TABLE 2.
Statistics for x-ray data collection and structural refinement
Values in parentheses are for the highest resolution shell.
| Statistic | Open form | Open form with Fuc | Closed form |
|---|---|---|---|
| Protein Data Bank ID code | 4PSP | 4PSR | 4NI3 |
| Spacegroup | P1 | P1 | P1 |
| Cell dimensions | |||
| a, b, c (Å) | 53.9, 75.9, 80.8 | 54.2, 76.0, 81.0 | 53.5, 75.5, 80.4 |
| α, β, γ (°) | 105.9, 107.2, 106.8 | 105.7, 107.3, 106.9 | 105.6, 107.2, 106.7 |
| Wavelength (Å) | 0.9786 | 0.9786 | 0.9787 |
| Resolution of data collection (Å) | 50.0-1.59 (1.59-1.56) | 50.0-1.38 (1.40-1.38) | 50.0-1.40 (1.42-1.40) |
| No. of reflections (measured/unique) | 575,637/148,010 | 833,789/214,983 | 736,291/198,786 |
| Completeness % (Å) | 96.9 (94.4) | 96.1 (93.2) | 95.4 (92.0) |
| Redundancy | 3.9 (3.1) | 3.9 (3.0) | 3.7 (3.5) |
| Rsyma | 0.062 (0.45) | 0.062 (0.62) | 0.051 (0.56) |
| I/σb | 21.5 (2.6) | 16 (1.8) | 18 (2.3) |
| Resolution range in refinement (Å) | 41.24-1.56 | 43.28-1.38 | 37.93-1.40 |
| No. of unique reflections (work/test) | 148,007/7,414 | 214,972/10,714 | 198,748/1,905 |
| Rcrystc | 13.5 (20.2) | 13.8 (23.6) | 14.5 (22.0) |
| Rfreed | 16.9 (24.8) | 16.6 (27.2) | 16.7 (29.3) |
| Mean coordinate errore (Å) | 0.14 | 0.14 | 0.13 |
| Rmsd bond length (Å) | 0.009 | 0.011 | 0.01 |
| Rmsd bond angles (°) | 1.2 | 1.4 | 1.2 |
| Average B value (Å2) (overall/protein/waters/ligand) | 19.7/17.4/31.3/27.2 | 19.3/17.0/31.6/25.3 | 21.7/19.9/33.3/27 |
| No. of non-hydrogen atoms | 11,810 | 11,877 | 11,227 |
| No. of protein atoms | 9,752 | 9,807 | 9,548 |
| No. of waters | 1,786 | 1,765 | 1,402 |
| No. of ligands and sugars | 6 Tris, 4 glycerol, 7 GlcNAc, 9 mannose 3 Na+ | 2Fuc, 6 Tris, 4 glycerol, 7 GlcNAc, 9 mannose, 3 Na+ | 7 Tris, 4 glycerol, 7 GlcNAc, 8 mannose 3 Na+ |
| Ramachandran Statisticsf (%) | 97.55, 2.37, 0.08 | 97.80, 2.20, 0 | 97.66, 2.34, 0 |
a Rsym = Σhkl Σi |Ii(hkl) − 〈I(hkl)〉|/Σhkl ΣiIi(hkl), where Ii(hkl) is the intensity of an individual measurement of the symmetry related reflection, and 〈I(hkl)〉 is the mean intensity of the symmetry related reflections.
b I/σ is defined as the ratio of averaged value of the intensity to its standard deviation.
c Rcryst = Σhkl‖Fobs| − |Fcalc‖/Σhkl|Fobs|, where Fobs and Fcalc are the observed and calculated structure-factor amplitudes.
d Rfree was calculated as Rcryst using randomly selected small fractions of the unique reflections (5%, open form; 1%, closed form) that were omitted from the structure refinement.
e Mean coordinate error was calculated based on maximum likelihood.
f Ramachandran statistics indicate the percentage of residues in the most favored, additionally allowed and outlier regions of the Ramachandran diagram as defined by MOLPROBITY.