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Crude water-extracted pectin (WEP) isolated from creeping fig seeds were mainly fractionated into WEP-0.3 and WEP-0.4 fractions. Fractions were confirmed to be nonstarch, nonreducing sugars, nonpolyphenols and protein-unbounded acidic polysaccharides. Interestingly, a significant difference in solubility was found between WEP-0.3 (higher solubility than WEP) and WEP-0.4 (remarkably insoluble), which was consistent with the amorphous and porous sponge-like structure of WEP-0.3 as well as the crystalline and dense rod-like state of WEP-0.4. However, the result of the FT-IR spectra was contradicted by the solubility of WEP-0.4, which possessed the lowest degree of methoxylation and ought to possess the highest solubility. Through mineral analysis, a considerably high content of Ca2+ was found in WEP-0.4, suggesting that the low solubility of WEP-0.4 was probably attributable to the formation of microgels during dialysis. Therefore, metal divalent cations in the dialysate were suggested to be depleted for the dialysis of low methoxyl pectin.