4TWS

Gadolinium Derivative of Tetragonal Hen Egg-White Lysozyme at 1.45 A Resolution

4TWS の概要

• エントリーDOI: 10.2210/pdb4tws/pdb
• 分子名称: Lysozyme C, GADOLINIUM ATOM, 10-((2R)-2-HYDROXYPROPYL)-1,4,7,10-TETRAAZACYCLODODECANE 1,4,7-TRIACETIC ACID, ... (6 entities in total)
• 機能のキーワード: lysozyme, gadolinium, hydrolase
• 由来する生物種: Gallus gallus (Chicken)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 16592.13

構造登録者

Holton, J.M.,Classen, S.,Frankel, K.A.,Tainer, J.A. (登録日: 2014-07-01, 公開日: 2014-08-20, 最終更新日: 2024-11-20)

主引用文献

Holton, J.M.,Classen, S.,Frankel, K.A.,Tainer, J.A.
The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures.
Febs J., 281:4046-4060, 2014

PubMed Abstract: In macromolecular crystallography, the agreement between observed and predicted structure factors (Rcryst and Rfree ) is seldom better than 20%. This is much larger than the estimate of experimental error (Rmerge ). The difference between Rcryst and Rmerge is the R-factor gap. There is no such gap in small-molecule crystallography, for which calculated structure factors are generally considered more accurate than the experimental measurements. Perhaps the true noise level of macromolecular data is higher than expected? Or is the gap caused by inaccurate phases that trap refined models in local minima? By generating simulated diffraction patterns using the program MLFSOM, and including every conceivable source of experimental error, we show that neither is the case. Processing our simulated data yielded values that were indistinguishable from those of real data for all crystallographic statistics except the final Rcryst and Rfree . These values decreased to 3.8% and 5.5% for simulated data, suggesting that the reason for high R-factors in macromolecular crystallography is neither experimental error nor phase bias, but rather an underlying inadequacy in the models used to explain our observations. The present inability to accurately represent the entire macromolecule with both its flexibility and its protein-solvent interface may be improved by synergies between small-angle X-ray scattering, computational chemistry and crystallography. The exciting implication of our finding is that macromolecular data contain substantial hidden and untapped potential to resolve ambiguities in the true nature of the nanoscale, a task that the second century of crystallography promises to fulfill.

PubMed: 25040949
DOI: 10.1111/febs.12922

実験手法

X-RAY DIFFRACTION (1.45 Å)