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[ccp4bb]: non-specifically bound heavy atom?
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Dear all,
I have a question related to heavy atom derivitives.
I have soaked a crystal in 1mM ethylmercury phosphate for 2 days
(There is 1 cys in the 38kD protein.) The Hg data
are reasonably good to 4A (data statistics see below, 92% complete,
>60% of the data have more than 2 observations). After
I scaled the Hg data with the native data set, the overall Riso
is 18.7% (see below for statistics from scaleit). But the difference
patterson map does not have any peaks standing out. The highest
peaks on harker sections are only about 3sigma. I am a little
puzzled. Somebody has suggested to me that the Hg compound could
be binding to the protein surface non-specifically, that is why
I couldn't see any peak in the difference patterson. I am wondering
if anybody else had similar experience before.
I greatly appreciate your comments/suggestions on the situation.
The question following this is: we are going to a synchrotron in a few
days. I imagine I still will see a Hg peak in the absorption spectrum
even if it is non-specifically bound. Am I wasting time in trying to
collect a Hg MAD data set?
Thank you very much for your help.
Sincerely, Rui.
scalepack output:
Shell Lower Upper Average Average Norm. Linear Square
limit Angstrom I error stat. Chi**2 R-fac R-fac
30.00 8.56 18716.3 586.0 166.3 9.923 0.054 0.070
8.56 6.82 5377.2 282.6 126.8 1.600 0.063 0.069
6.82 5.96 2321.7 189.7 127.0 1.145 0.084 0.085
5.96 5.42 2097.3 205.4 136.1 0.977 0.086 0.078
5.42 5.04 2087.1 234.5 145.7 0.821 0.088 0.076
5.04 4.74 2233.7 311.6 159.9 0.643 0.096 0.088
4.74 4.50 2502.8 366.1 174.0 0.599 0.091 0.086
4.50 4.31 2010.1 532.4 186.0 0.400 0.110 0.096
4.31 4.14 1407.5 480.6 201.2 0.397 0.148 0.132
4.14 4.00 1230.8 386.5 215.3 0.612 0.174 0.152
All reflections 4013.7 357.4 163.7 1.681 0.077 0.073
Scaleit output:
<4SSQ/LL> Res NRef <FP**2> Sc_kraut SCALE RFAC RF_I Wted_R <diso> max(diso)
0.008 11.3 39 469798. 1.154 1.107 0.204 0.308 0.239 124.1 473
0.011 9.6 165 334552. 1.049 1.009 0.191 0.291 0.254 96.9 449
0.014 8.4 203 236577. 0.993 0.963 0.183 0.289 0.244 76.7 283
0.017 7.6 215 118957. 1.048 1.005 0.205 0.294 0.231 59.8 317
0.020 7.0 242 60026. 1.049 1.007 0.202 0.321 0.171 43.1 185
0.023 6.5 260 44330. 1.046 0.996 0.209 0.345 0.168 39.0 192
0.027 6.1 271 42172. 1.050 1.016 0.189 0.303 0.153 33.8 162
0.030 5.8 304 36710. 1.063 1.027 0.189 0.290 0.164 31.3 125
0.033 5.5 317 47045. 1.064 1.039 0.165 0.233 0.145 29.7 204
0.036 5.3 313 47731. 1.052 1.024 0.181 0.261 0.159 32.3 132
0.039 5.1 315 44372. 1.048 1.020 0.175 0.264 0.137 31.4 141
0.042 4.9 319 54105. 1.058 1.022 0.189 0.299 0.148 37.0 165
0.045 4.7 311 67814. 1.041 1.012 0.173 0.283 0.121 38.2 185
0.048 4.5 306 69882. 1.048 1.023 0.167 0.273 0.113 37.2 191
0.052 4.4 304 65554. 1.046 1.019 0.175 0.280 0.120 37.7 147
0.055 4.3 311 49965. 1.008 0.985 0.176 0.279 0.098 33.9 143
0.058 4.2 290 46024. 1.072 1.041 0.202 0.329 0.121 37.4 176
0.061 4.1 435 45158. 1.053 1.024 0.203 0.314 0.120 36.9 263
THE TOTALS 4920. 74753. 1.046 1.012 0.187 0.291 0.169 41.0 473.