4LR3
Crystal structure of E. coli YfbU at 2.5 A resolution
Summary for 4LR3
| Entry DOI | 10.2210/pdb4lr3/pdb |
| Descriptor | protein YfbU, MAGNESIUM ION, PHOSPHATE ION, ... (4 entities in total) |
| Functional Keywords | helical tetramer, apoptosis |
| Biological source | Escherichia coli |
| Total number of polymer chains | 16 |
| Total formula weight | 315925.50 |
| Authors | Wang, J.,Wing, R.A. (deposition date: 2013-07-19, release date: 2014-04-30, Last modification date: 2024-02-28) |
| Primary citation | Wang, J.,Wing, R.A. Diamonds in the rough: a strong case for the inclusion of weak-intensity X-ray diffraction data. Acta Crystallogr.,Sect.D, 70:1491-1497, 2014 Cited by PubMed Abstract: Overwhelming evidence exists to show that the inclusion of weak-intensity, high-resolution X-ray diffraction data helps improve the refinement of atomic models by imposing strong constraints on individual and overall temperature B factors and thus the quality of crystal structures. Some researchers consider these data to be of little value and opt to discard them during data processing, particularly at medium and low resolution, at which individual B factors of atomic models cannot be refined. Here, new evidence is provided to show that the inclusion of these data helps to improve the quality of experimental phases by imposing proper constraints on electron-density models during noncrystallographic symmetry (NCS) averaging. Using electron-density correlation coefficients as criteria, the resolution of data has successfully been extended from 3.1 to 2.5 Å resolution with redundancy-independent merging R factors from below 100% to about 310%. It is further demonstrated that phase information can be fully extracted from observed amplitudes through de novo NCS averaging. Averaging starts with uniform density inside double-shelled spherical masks and NCS matrices that are derived from bound heavy-atom clusters at the vertices of cuboctahedrally symmetric protein particles. PubMed: 24816117DOI: 10.1107/S1399004714005318 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.5 Å) |
Structure validation
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