[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

[ccp4bb]: non-specifically bound heavy atom?



***  For details on how to be removed from this list visit the  ***
***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***

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.