Case study of using the single-atom R1 method to solve a small protein structure

A small protein structure would not yield a solution via the single-atom R1 (sR1) method. A salient sign of trouble was that many atoms were dubiously accepted into the model because their introduction caused the sR1 value to increase. A plausible hypothesis is that this was very likely due to a hidden solvent diffraction effect. After accounting for this hidden solvent effect via padding additional C atoms, this small protein structure now has been successfully solved by the sR1 method. Further analysis of the protein crystal density indicated that the above successful padding of C atoms had over-accounted for the solvent content. However, empirical observations have indicated that, when an initial application of the sR1 method shows that many atoms are not welcomed into the model, padding numerous C atoms (even if over-accounting for the solvent content) benefits the sR1 calculation by making spotting plausible fragments more reliable and/or making the resulting model more complete.