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Simulated-1g1c: Difference between revisions
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→Solving the structure
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Final R-work = 0.2170, R-free = 0.2596 | Final R-work = 0.2170, R-free = 0.2596 | ||
which appears reasonable. | which appears reasonable. | ||
== Notes == | |||
=== Towards better completeness: using the first two frames === | |||
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 XDS.INP : | |||
DATA_RANGE=1 2 | |||
and in XSCALE.INP we insert | |||
NBATCH=2 | |||
after each INPUT_FILE line. The reason for this is that by default, XSCALE establishes scalefactors every DELPHI (default: 5) degrees, but here we want scalefactors for every frame, because the radiation damage is so strong. This gives: | |||
NOTE: Friedel pairs are treated as different reflections. | |||
SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION | |||
RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR R-FACTOR COMPARED I/SIGMA R-meas Rmrgd-F Anomal SigAno Nano | |||
LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected Corr | |||
8.05 1922 467 476 98.1% 4.2% 6.6% 1888 20.04 4.8% 2.8% 84% 1.887 142 | |||
5.69 3494 864 882 98.0% 4.5% 6.8% 3429 18.67 5.2% 3.1% 83% 1.635 297 | |||
4.65 4480 1111 1136 97.8% 5.3% 6.7% 4395 18.89 6.1% 3.5% 66% 1.347 406 | |||
4.03 5197 1325 1357 97.6% 6.2% 6.8% 5101 18.37 7.1% 4.3% 43% 1.156 499 | |||
3.60 5916 1500 1533 97.8% 6.9% 7.1% 5804 17.83 8.0% 4.7% 36% 1.083 572 | |||
3.29 6601 1657 1694 97.8% 7.6% 7.3% 6476 17.26 8.7% 4.9% 24% 1.029 634 | |||
3.04 7081 1789 1830 97.8% 9.1% 8.0% 6949 15.50 10.4% 6.4% 17% 1.011 693 | |||
2.85 7684 1946 1979 98.3% 10.9% 9.9% 7530 12.95 12.5% 8.1% 16% 0.950 751 | |||
2.68 8101 2062 2100 98.2% 13.1% 12.1% 7935 11.18 15.0% 10.5% 10% 0.888 795 | |||
2.55 8355 2156 2201 98.0% 15.2% 14.9% 8182 9.69 17.5% 12.3% 6% 0.867 837 | |||
2.43 9195 2327 2376 97.9% 18.2% 18.6% 9003 8.20 20.8% 15.4% 6% 0.837 904 | |||
2.32 9495 2377 2428 97.9% 21.3% 21.9% 9304 7.42 24.4% 18.4% 6% 0.800 934 | |||
2.23 9939 2499 2551 98.0% 23.0% 23.3% 9753 7.13 26.4% 19.0% 4% 0.818 987 | |||
2.15 10219 2577 2622 98.3% 25.4% 25.9% 9992 6.63 29.1% 20.6% 1% 0.797 998 | |||
2.08 10712 2704 2766 97.8% 29.4% 30.8% 10508 5.80 33.8% 25.1% 4% 0.793 1071 | |||
2.01 10900 2778 2839 97.9% 30.8% 31.2% 10649 5.50 35.3% 26.2% 4% 0.828 1060 | |||
1.95 11361 2878 2937 98.0% 36.7% 38.2% 11134 4.71 42.1% 31.5% 1% 0.768 1136 | |||
1.90 11641 2943 3000 98.1% 42.7% 45.1% 11405 4.12 49.1% 38.7% -1% 0.775 1165 | |||
1.85 12028 3069 3123 98.3% 54.0% 60.4% 11760 3.19 62.1% 47.5% 5% 0.735 1196 | |||
1.80 11506 3003 3173 94.6% 62.1% 70.6% 11229 2.72 71.6% 60.6% -2% 0.709 1148 | |||
total 165827 42032 43003 97.7% 12.8% 13.3% 162426 8.79 14.7% 15.7% 15% 0.881 16225 | |||
showing that the anomalous completeness, and even the quality of the anomalous signal, can indeed be increased. I doubt, however, that going to three or more frames would improve things even more. | |||
=== 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 this translates into a almost centrosymmetric arrangement of substructure sites (check with [http://cci.lbl.gov/cctbx/phase_o_phrenia.html]). Indeed, the original structure was solved using molecular replacement. | |||