Aceclofenac and interactions analysis in the crystal and COX protein active site

Heterogeneous Composition of Oxygen-Evolving Complexes in Crystal Structures of Dark-Adapted Photosystem II

“…We cannot apply B -factor blurring to these structures to match those of very large macromolecules because if we do so, we have only a single Bragg reflection below 2.0 Å that still contains the information about the electron number. In fact, reciprocal space multipolar model refinement in general could not result in a reliable number of valence electrons, either, for crystal structures even at 0.37 Å resolution . An analysis of the deviation of multipolar model refined structure factors from spherically averaged amplitudes for carbonyl O atoms at 0.37 Å resolution using the method described in this study shows that the largest aspherical deviations are near 3.0 Å resolution and that the deviation largely disappears at 2.0 Å resolution.…”

“…The quality of the atomic models used for calculation of omit ED maps does affect the accuracy of the absolute values of ENs determined, more so for the absolute ENs than for the relative ENs. For small molecules, model R -factors of crystal structures are refined to 1–2% at subangstrom resolution. ,,, However, model R -factors for protein structures are much larger. For example, the cross-validation free R -factor for the 6jlj structure is 19.8% at 2.15 Å resolution, while for the 6w1o structure, it is 24.0% at 2.08 Å resolution. , Therefore, the results obtained for the 6jlj structure should be more accurate and more reliable than those for 6w1o. , Here, we use one of the metal ions (Mn2 of each OEC) as an internal reference, which improves greatly the accuracy and reliability of relative ENs because many modeling errors tend to cancel out (see the Supporting Information).…”

“…We can determine the overall variance only from the mean Gaussian terms (⟨ B + b i ⟩). Analytically fitted Gaussian parameters cannot distinguish between b i and B terms, nor can we decompose them unless diffraction data are measured at sub-angstrom resolution with the atomic B value becoming very small. ,, …”

“…Analytically fitted Gaussian parameters cannot distinguish between b i and B terms, nor can we decompose them unless diffraction data are measured at sub-angstrom resolution with the atomic B value becoming very small. 22,23,29 In the absence of model phase errors (as in error-free computer simulations), the maximal size of the omit F o − F c ED peak is only approximately half of its full ED peak, 30 which can be evaluated using vector difference Fourier maps that would require knowledge of form factors and the B-factor of the atom in question. In the presence of modeling errors, the size of the ED peak decreases further.…”

Refinements on electron diffraction data of β-glycine in MoPro: a quest for an improved structure model

“…The same atomic numbering scheme was used in further analysis. structure and charge density refinement software utilized in the past for various studies including small organic and macromolecular protein systems (Guillot et al, 2001;Jelsch et al, 2005Jelsch et al, , 2020Guillot et al, 2008;Bouhmaida et al, 2009;Niranjana Devi et al, 2017). Aspherical TAAM refinement using ELMAM2 database transfer on X-ray experimental data in MoPro is a very convenient and user-friendly tool (Zarychta et al, 2007;Domagała et al, 2012;Bibila Mayaya Bisseyou et al, 2012).…”