Is this common to MAD data? Have other people observed this behavior?
Is it indicative of either a data processing or scaling problem?
Background:
3 wavelengths of complete and redundant Se MAD data. By redundant,
I
mean at least 2-4 measurements for both I+ and I-, or 4-8 measurements
for I. The data was integrated with Denzo, each wavelength was
scaled
using scalepack, and then brought into ccp4 using scalepack2mtz.
Prior
to scaleit, the data was passed through sortmtz, truncate, and cad.
Scaling in scalepack used the 'scale anomalous' card for a few rounds
of scaling, followed by a final round of 'anomalous'.
The anomalous signal in these data sets is sufficient to find Se sites
via Shake-n-Bake and to be handled well by mlphare. The FOMs
for
centric reflections are much weaker than the acentrics - I suspect
this
is a result of the isomorphous differences shown below. A table
of FOMs
is also appended.
Electron density maps following solvent flattening and histogram
matching in dm show obvious solvent channels and reasonable protein
density. However, the protein density is not readily traceable.
Thanks for any help you can offer,
Isomorphous Differences
-----------------------
Derivative title:
FP= FP_se3a FPH= FP_se1a SIGFP_se1a DANO_se1a
SIGDANO_se1a
d -224 -196 -168 -140 -112
-84 -56 -28 0
28 56 84 112
140 168 196 224
18.97
0 0 0
0 0 0
0 0 0
0 0 0
0 0 0
0 0
10.95
0 0 0
0 0 0
0 0 0
0 0 0
0 0 0
0 0
8.49 0 0
0 0 0
0 1 15 161
401 126 26 2
0 0 0
0
7.17 0 0
0 0 0
0 1 33 320
700 157 9 1
2 1 0
0
6.32 0 0
0 0 0
0 3 42 371
783 194 13 1
1 0 0
0
5.72 0 0
0 0 1
0 5 40 358
807 312 40 1
0 0 0
0
5.26 0 0
0 0 0
0 2 27 245
722 578 113 15
3 0 0
0
4.90 0 0
0 0 0
0 3 25 207
586 668 268 84
16 3 1
0
4.60 0 0
0 0 0
1 5 44 194
491 642 418 141 32
14 1 1
4.35 0 0
0 0 0
0 5 42 178
443 688 485 186 51
12 4 0
4.14 0 0
0 0 0
1 6 52 213
504 676 484 206 62
20 2 1
3.96 0 0
0 0 0
2 8 72 255
514 669 500 213 63
13 1 1
3.79 0 0
0 0 1
2 13 105 291 531
676 502 221 53
9 1 3
3.65 0 0
0 0 1
0 23 99 285
553 663 540 250 70
10 2 2
3.52 0 0
0 1 3
2 25 102 338 598
697 541 228 87
12 5 0
3.41 0 0
0 0 0
4 25 114 366 575
683 551 265 79
25 2 3
3.30 0 0
0 0 1
6 28 118 405 680
620 517 263 110 15
4 2
3.21 0 0
0 1 0
3 9 103 468
777 720 497 230 64
11 4 0
3.12 0 0
1 1 0
4 12 112 483 922
707 442 181 61
19 3 0
3.04 0 0
0 0 0
2 14 112 771 1622
1056 460 200 61
18 2 0
Total 0 0 1 3 7 27 188 1257 5909 12209 10532 6406 2688 815 182 32 13
Anomolous Differences
---------------------
d -136 -119 -102 -85
-68 -51 -34 -17
0 17 34 51
68 85 102 119 136
18.97
0 0 0
0 0 0
0 0 0
0 0 0
0 0 0
0 0
10.95
0 0 0
0 0 0
0 0 0
0 0 0
0 0 0
0 0
8.49 0 0
1 3 8
24 70 141 246 131
70 28 8
2 0 0
0
7.17 0 0
1 3 15 52
121 217 393 233 127
39 21 2
0 0 0
6.32 0 0
1 1 15 53
148 287 434 276 137
42 12 2
0 0 0
5.72 0 0
0 1 12 45
147 288 500 354 158
49 8 2
0 0 0
5.26 0 0
1 1 14 39
144 386 539 362 147
56 14 2
0 0 0
4.90 0 1
3 4 15 49
177 403 612 392 147
44 11 2
1 0 0
4.60 0 0
2 7 19 46
196 393 682 434 142
41 14 5
2 0 1
4.35 0 2
2 7 26 66
198 413 679 444 174
54 18 7
4 0 0
4.14 1 0
4 11 39 84
163 457 691 461 195
80 24 14 3
0 0
3.96 3 4
7 24 43 88
226 418 660 452 237
85 42 16 4
2 0
3.79 5 3
11 30 55 117
243 442 608 436 247
117 40 36 8
6 4
3.65 7 10 18
31 66 149 259 422
577 410 272 140 71
34 24 4
4
3.52 7 7
21 31 89 153
303 419 610 422 282
149 79 46 16
4 1
3.41 14 11 28
45 103 160 286 427
572 418 293 175 83
49 14 11 3
3.30 16 16 22
46 96 179 313 430
536 422 342 168 97
53 21 10 2
3.21 12 11 26
58 103 194 321 463
594 464 303 178 90
48 14 3
5
3.12 5 11 16
40 99 186 320 488
646 477 318 184 91
43 16 7
1
3.04 6 12 18
46 115 208 461 814
1081 746 414 218 107
40 20 7
5
Total
76 88 182 389 932
1892 4096 7308 10660 7334 4005 1847
830 403 147 54
26
Resolution in angstroms
7.90
6.53 5.57 4.85 4.30
3.86 3.50 3.20
Number of Measurements
phased -ACENTRIC
TOTAL
2037
1683 2408 3228 4206
5281 6523 7834
33200
Mean Figure of
Merit
0.5247
0.5885 0.5170 0.4405 0.3459 0.2242 0.1499
0.1017 0.2753
Number of Measurements
phased -CENTRIC
TOTAL
149 78 98
111 126 143
158 177
1040
Mean Figure of
Merit
0.3936
0.2989 0.2280 0.1838 0.1644 0.0908 0.0637
0.0394 0.1687
Number of Measurements
phased -ALL
TOTAL
2186
1761 2506 3339 4332
5424 6681 8011
34240
Mean Figure of
Merit
0.5158
0.5757 0.5057 0.4320 0.3406 0.2207 0.1479
0.1003 0.2720
-- Dr. Linda Hannick, Structural Biology National Institute of Allergy and Infectious Diseases National Institutes of Health 12441 Parklawn Drive 301-496-3792 Voice Rockville, MD 20852 301-402-0284 FAX