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Simulated-1g1c: Difference between revisions
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== Notes == | == Notes == | ||
=== Towards better completeness: using the first two frames === | === Towards better completeness: using the first two frames instead of only the first === | ||
We might want better (anomalous) completeness than what is given by only the very first frame of each dataset. To this end, we change in the XDS.INP part of our script : | We might want better (anomalous) completeness than what is given by only the very first frame of each dataset. To this end, we change in the XDS.INP part of our script : | ||
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Final R-work = 0.2244, R-free = 0.2504 | Final R-work = 0.2244, R-free = 0.2504 | ||
so: better R-free is obtained from better data. | so: '''better R-free is obtained from better data.''' | ||
The statistics from SHELXD and SHELXE don't look better - they were already quite good with a single frame per dataset. The statistics printed by SHELXE (for the correct hand) are: | The statistics from SHELXD and SHELXE don't look better - they were already quite good with a single frame per dataset. The statistics printed by SHELXE (for the correct hand) are: | ||
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6 0.5158 0.4788 0.0406 4.7 5/1.45 3/4.94 4/7.85 1/21.38 5/23.30 | 6 0.5158 0.4788 0.0406 4.7 5/1.45 3/4.94 4/7.85 1/21.38 5/23.30 | ||
Using | === Why this is difficult to solve with SAD phasing === | ||
In the original publication ("Structural evidence for a possible role of reversible disulphide bridge formation in the elasticity of the muscle protein titin" Mayans, O., Wuerges, J., Canela, S., Gautel, M., Wilmanns, M. (2001) Structure 9: 331-340 ) we read: | |||
"This crystal form contains two molecules in the asymmetric unit. They are related by a noncrystallographic two-fold axis, parallel to the crystallographic b axis, located at X = 0.25 and Z = 0.23. This arrangement results in a peak in the native Patterson map at U = 0.5, V = 0, W = 0.47 of peak height 26 σ (42% of the origin peak)." | |||
Unfortunately, the arrangement of substructure sites has translational symmetry, and may be related to a centrosymmetric arrangement. Indeed, the original structure was solved using molecular replacement. | |||
Using the four sites as given by SHELXE (and default parameters otherwise), I obtained from the [http://cci.lbl.gov/cctbx/phase_o_phrenia.html cctbx - Phase-O-Phrenia server] the following | |||
Plot of relative peak heights: | Plot of relative peak heights: | ||
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so the strongest peak corresponds to the translation of molecules (0,0.5,0) but the origin peak is at 1/2 of that size, which appears significant. (I cannot interpret the plot of relative peak heights, though <big>☹</big>) | so the strongest peak corresponds to the translation of molecules (0,0.5,0) but the origin peak is at 1/2 of that size, which appears significant. (I cannot interpret the plot of relative peak heights, though <big>☹</big>) | ||