Adams et al. Respond

Abstract

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Strategies for carbohydrate model building, refinement and validation

“…More recently, another study reported a worrying situation affecting ring conformation , using N-glycan-forming d-pyranosides as an example, although the results clearly extend not only to all pyranose sugars but to every ligand with a saturated six-membered ring. In general, the software tools that deal admirably with proteins (Murshudov et al, 2011;Adams et al, 2011;Emsley et al, 2010;Blanc et al, 2004;Brü nger et al, 1998), and nucleic acids to some extent, appear to have problems handling ligands at lower resolution (Reynolds, 2014;Liebeschuetz et al, 2012;Perola & Charifson, 2004), with thousands of structures showing angle and torsional strains that cannot be supported unequivocally by the experimental data. Pyranosides, and indeed all saturated cyclic compounds, might not necessarily show such strains, but can be spuriously locked into secondary energy minima (typically boat conformations) that may only show transannular strain after rounds of model refinement against low-resolution data.…”

Structural and biophysical characterization of the α-carbonic anhydrase from the gammaproteobacteriumThiomicrospira crunogenaXCL-2: insights into engineering thermostable enzymes for CO2sequestration

“…MR solutions were calculated using PHENIX (McCoy et al, 2007;Adams et al, 2011). The starting phases of the TcruCA model yielded a unique solution comprising of four molecules in the asymmetric unit ( Supplementary Fig.…”

“…Each chain contained 230 amino acids, corresponding to residues 75-304 of full-length TcruCA. Refinement was also completed using PHENIX (Adams et al, 2011). Each refinement was performed with 5% of the unique reflections excluded for the calculation of R free (Brü nger, 1992).…”

Crystallographic studies of the structured core domain of Knr4 fromSaccharomyces cerevisiae

“…Data processing was initially performed automatically with autoPROC (Vonrhein et al, 2011) and was further optimized with XDS (Kabsch, 2010) 10.5 6.3 Buffer composition of protein solution 0.15 M NaCl, 0.1 M Tris-HCl pH 7.5 0.15 M NaCl, 0.1 M Tris-HCl pH 7.5 Composition of reservoir solution 1.2 M ammonium sulfate, 0.1 M MES-NaOH pH 5.5 1.4 M ammonium sulfate, 0.1 M MES-NaOH pH 6.0 Volume and ratio of drop 2 ml + 2 ml 2 ml protein solution + 1 ml reservoir solution Volume of reservoir (ml) 500 500 performed with CCP4 (Winn et al, 2011), PHENIX (Adams et al, 2011) and SHELX (Sheldrick, 2010).…”