Methods used in the structure determination of bovine mitochondrial F1 ATPase.

By J. Abrahams, A. Leslie. 1996

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Overview of the CCP4 suite and current developments (2011, methodology): “Phase improvement is carried out by SOLOMON (Abrahams & Leslie, 1996), DM (Cowtan et al., 2001) or Pirate (Cowtan, 2000) and automated model building by Buccaneer (Cowtan, 2006; Cowtan, 2008) or ARP/wARP (Langer et al., 2008).”
Structure of Functionally Activated Small Ribosomal Subunit at 3.3 Å Resolution (2000, methodology): “The overall figure of merit (FOM) was 0.48 after MIRAS phasing with SHARP, and 0.78 after density modification with SOLOMON. a Isomorphous/anomalous.”
Phase Retrieval Using Alternating Minimization (2013, methodology): “We also deﬁne Ph ( z ) for every w 1 , w 2 ∈ C n . inally, we use the shorthand wlog for without loss of generality and whp for with high probability.”
Crystal structure and mechanism of a calcium-gated potassium channel (2002, methodology): “; initial phases were improved by solvent flattening with SOLOMO”
Can I solve my structure by SAD phasing? Anomalous signal in SAD phasing (2016, methodology): “This electron-density map is normally then improved by density-modification techniques (Wang, 1985; Cowtan & Main, 1996; Abrahams & Leslie, 1996; Terwilliger, 2000; Cowtan, 2010) and interpreted in terms of an atomic model (see, for example, Jones et al., 1991; Perrakis et al., 1999; Emsley et al.,…”
Crystal structure of the human angiotensin-converting enzyme–lisinopril complex (2003, methodology): “0 A) by iterative solvent flattening, phase combination, and phase extension with the program SOLOMO”
Recent developments in classical density modification (2010, methodology): “This basic scheme has been implemented with some refinements in the DM (Cowtan et al., 2001) and SOLOMON (Abrahams & Leslie, 1996) software, with some variations, as well as in many other packages.”
Knowledge-based real-space explorations for low-resolution structure determination. (2006, methodology): “Four gold sites were detected with the Shake‘N’Bake program (Weeks and Miller, 1999), with phases determined by SHARP (Bricogne et al., 2003) and the resultant density modified by SOLOMON ( Abrahams and Leslie, 1996 ).”
Recent developments in phasing and structure refinement for macromolecular crystallography (2009, methodology): “Recently density modification procedures have been greatly improved through statistical treatments that reduce bias toward the starting map by solvent flipping [30] or maximum-likelihood techniques [31–33].”