Accuracy and precision in protein crystal structure analysis: two independent refinements of the structure of poplar plastocyanin at 173 K

Abstract

The structure of the copper protein plastocyanin from poplar leaves (Populus nigra var. italica) at 173 K has been subjected to two independent refinements, usin~ a single set of synchrotron X-ray data at 1.6 A resolution.Energy-restrained refinement using the program EREF resulted in lower root-mean-square deviations from ideal geom- Greater order in the solvent region is indicated by the location of 79 more solvent sites, the identification of extensive networks of hydrogen-bonded rings of solvent molecules, and a general decrease in the thermal parameters. Within the unit cell, the protein molecules are significantly translated and rotated from their positions at ambient temperature. An

Effect of covalent links on the structure, spectra, and redox properties of myeloperoxidase – A density functional study

“…The crystal structure of this state shows a water molecule at a Fe-O distance of 2.90 Å [4]. This is much longer than in any of the optimized ground states ($2.10 Å for Fe II are around 0.39, 2.08, and 2.10 Å , which are reasonable considering the accuracy of the crystal structure ($0.1 Å [46,47]) and the theoretical calculations ($0.05 Å [48]). However, the distortion of the porphyrin ring is larger in the crystal structure than in the optimized models (Por oop is 0.28 Å compared to 0.08 Å ).…”

Error Estimates of Protein Structure Coordinates and Deviations from Standard Geometry by Full-Matrix Refinement ofγB- andβB2-Crystallin

“…Fields et al (1994) performed two independent refinements, using different refinement programs, using a single set of synchrotron X-ray data at 1.6 A resolution. The r.m.s.…”

The Importance of the MM Environment and the Selection of the QM Method in QM/MM Calculations

“…Indeed, in the case of metal complexes, errors in M-L bond lengths are typically less than 0.07 Å (Neese, 2006;Ryde, 2003Ryde, , 2007Shen & Ryde, 2004;Sigfridsson, Olsson, & Ryde, 2001;Sigfridsson & Ryde, 2002). Notably, this compares favorably with errors of 0.1 Å and even 0.3 Å that have been seen in crystallographic methods (Cruickshank, 1999;Fields et al, 1994;Nilsson, Lecerof, Sigfridsson, & Ryde, 2003). Indeed, hybrid DFT methods, in particular B3LYP, have become the standard tools of choice for computational investigations on enzymes and metalloenzymes (Becke, 1993a(Becke, , 1993bLee, Yang, & Parr, 1988;Siegbahn, 2006).…”