4FE1

Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution

Summary for 4FE1

• Entry DOI: 10.2210/pdb4fe1/pdb
• Related: 1JB0 3LW5 3PCQ
• Descriptor: Photosystem I P700 chlorophyll a apoprotein A1, Photosystem I reaction center subunit XI, Photosystem I reaction center subunit XII, ... (19 entities in total)
• Functional Keywords: photosystem, photosynthesis, membrane protein, chlorophyll, chromophore, electron transport, metal-binding, photosystem i, thylakoid, transmembrane, electron transfer, membrane, thylakoidmembrane
• Biological source: Thermosynechococcus elongatus; More
• Cellular location: Cellular thylakoid membrane; Multi-pass membrane protein (By similarity): P0A405 P0A407; Cellular thylakoid membrane; Multi-pass membrane protein (Probable): Q8DGB4 P0A425; Cellular thylakoid membrane; Single-pass membrane protein (Probable): P0A403; Cellular thylakoid membrane; Peripheral membrane protein; Cytoplasmic side (By similarity): P0A415; Cellular thylakoid membrane; Peripheral membrane protein (By similarity): P0A423; Cellular thylakoid membrane; Single-pass membrane protein (By similarity): P0A427 P0A429
• Total number of polymer chains: 12
• Total formula weight: 359700.13

Authors

Fromme, R.,Adams, P.D.,Fromme, P.,Levitt, M.,Schroeder, G.F.,Brunger, A.T. (deposition date: 2012-05-29, release date: 2012-08-15, Last modification date: 2023-09-13)

Primary citation

Brunger, A.T.,Adams, P.D.,Fromme, P.,Fromme, R.,Levitt, M.,Schroder, G.F.
Improving the accuracy of macromolecular structure refinement at 7 A resolution.
Structure, 20:957-966, 2012

PubMed Abstract: In X-ray crystallography, molecular replacement and subsequent refinement is challenging at low resolution. We compared refinement methods using synchrotron diffraction data of photosystem I at 7.4 Å resolution, starting from different initial models with increasing deviations from the known high-resolution structure. Standard refinement spoiled the initial models, moving them further away from the true structure and leading to high R(free)-values. In contrast, DEN refinement improved even the most distant starting model as judged by R(free), atomic root-mean-square differences to the true structure, significance of features not included in the initial model, and connectivity of electron density. The best protocol was DEN refinement with initial segmented rigid-body refinement. For the most distant initial model, the fraction of atoms within 2 Å of the true structure improved from 24% to 60%. We also found a significant correlation between R(free) values and the accuracy of the model, suggesting that R(free) is useful even at low resolution.

PubMed: 22681901
DOI: 10.1016/j.str.2012.04.020

Experimental method

X-RAY DIFFRACTION (4.9228 Å)