I am currently trying to solve two datasets of two different protein-protein
complexes. One of the proteins is common to both complexes and there is a
deposited structure in the PDB (100% identical). The other proteins currently
have not been solved and share ~50% identity between them. Both complexes
crystallize in different space groups. All three proteins are ~12kDa. Both
datasets diffract to ~3-3.5A.
A) C2221 109.6 110.1 335.2 90 90 90 with around 9 copies of the complex.
B) I4122 131.6 131.6 257.1 90 90 90 with 5 copies of the complex.
I am slightly suspicious of Dataset A due to similar a and b lengths. Merging
in P4, results in higher Rmerges.
However in each case, searching with the common protein, results in Phaser
failing to find a single copy of the protein, despite TFZ scores of 8-12, due
to rejection during packing;
Dataset A
Packing Table
-------------
Solutions accepted if total number of clashes <= 5% of trace atoms
i.e. total number of clashes <= 5
AND if number of clashes <= 5% of trace atoms for each ensemble
i.e. ensemble1: number of clashes <= 5
# # #Clash Packs SpaceGroup Annotation
1 198 NO C 2 2 2 RFZ=2.9 TFZ=11.2
2 154 NO C 2 2 2 RFZ=2.3 TFZ=10.8
3 229 NO C 2 2 2 RFZ=2.6 TFZ=11.5
4 161 NO C 2 2 2 RFZ=2.5 TFZ=10.0
5 118 NO C 2 2 2 RFZ=2.4 TFZ=9.8
6 166 NO C 2 2 2 RFZ=2.9 TFZ=8.1
7 199 NO C 2 2 2 RFZ=2.6 TFZ=10.0
8 165 NO C 2 2 2 RFZ=2.5 TFZ=10.0
9 167 NO C 2 2 2 RFZ=2.4 TFZ=10.1
10 168 NO C 2 2 2 RFZ=2.5 TFZ=8.8
11 186 NO C 2 2 2 RFZ=2.4 TFZ=9.0
12 93 NO C 2 2 2 RFZ=2.5 TFZ=8.3
13 155 NO C 2 2 2 RFZ=3.1 TFZ=8.8
14 149 NO C 2 2 2 RFZ=2.9 TFZ=8.1
15 158 NO C 2 2 2 RFZ=2.6 TFZ=9.7
16 151 NO C 2 2 2 RFZ=2.6 TFZ=10.5
17 147 NO C 2 2 2 RFZ=3.1 TFZ=8.6
18 145 NO C 2 2 2 RFZ=2.4 TFZ=8.8
19 130 NO C 2 2 2 RFZ=2.4 TFZ=10.8
20 166 NO C 2 2 2 RFZ=2.9 TFZ=8.4
21 215 NO C 2 2 2 RFZ=2.4 TFZ=10.0
22 147 NO C 2 2 2 RFZ=2.6 TFZ=10.1
23 189 NO C 2 2 2 RFZ=2.6 TFZ=9.6
24 164 NO C 2 2 2 RFZ=2.5 TFZ=9.2
25 166 NO C 2 2 2 RFZ=2.6 TFZ=9.3
26 234 NO C 2 2 2 RFZ=2.4 TFZ=8.3
27 170 NO C 2 2 2 RFZ=2.4 TFZ=9.3
28 126 NO C 2 2 2 RFZ=2.6 TFZ=8.1
29 189 NO C 2 2 2 RFZ=2.5 TFZ=9.4
30 171 NO C 2 2 2 RFZ=2.3 TFZ=9.6
31 211 NO C 2 2 2 RFZ=2.5 TFZ=8.6
32 203 NO C 2 2 2 RFZ=2.5 TFZ=10.2
33 162 NO C 2 2 2 RFZ=2.4 TFZ=9.7
34 116 NO C 2 2 2 RFZ=2.6 TFZ=8.5
35 168 NO C 2 2 2 RFZ=2.5 TFZ=8.1
36 159 NO C 2 2 2 RFZ=2.4 TFZ=9.6
37 91 NO C 2 2 2 RFZ=2.5 TFZ=8.6
38 114 NO C 2 2 2 RFZ=2.5 TFZ=8.6
39 212 NO C 2 2 2 RFZ=2.4 TFZ=8.3
40 162 NO C 2 2 2 RFZ=2.4 TFZ=10.1
41 182 NO C 2 2 2 RFZ=2.9 TFZ=8.4
42 112 NO C 2 2 2 RFZ=2.5 TFZ=8.3
43 131 NO C 2 2 2 RFZ=2.4 TFZ=9.3
44 166 NO C 2 2 2 RFZ=2.3 TFZ=9.4
45 135 NO C 2 2 2 RFZ=2.4 TFZ=9.4
46 156 NO C 2 2 2 RFZ=2.5 TFZ=8.5
47 189 NO C 2 2 2 RFZ=2.5 TFZ=8.6
48 133 NO C 2 2 2 RFZ=2.5 TFZ=8.6
49 200 NO C 2 2 2 RFZ=2.5 TFZ=9.1
50 146 NO C 2 2 2 RFZ=2.6 TFZ=9.2
51 117 NO C 2 2 2 RFZ=2.4 TFZ=8.5
52 128 NO C 2 2 2 RFZ=2.5 TFZ=8.2
53 144 NO C 2 2 2 RFZ=2.4 TFZ=9.0
54 148 NO C 2 2 2 RFZ=2.5 TFZ=8.1
55 119 NO C 2 2 2 RFZ=2.4 TFZ=8.5
56 131 NO C 2 2 2 RFZ=2.4 TFZ=8.5
57 131 NO C 2 2 2 RFZ=2.5 TFZ=8.4
58 173 NO C 2 2 2 RFZ=2.6 TFZ=8.9
59 114 NO C 2 2 2 RFZ=2.6 TFZ=8.1
60 150 NO C 2 2 2 RFZ=2.4 TFZ=8.6
61 150 NO C 2 2 2 RFZ=2.4 TFZ=8.4
62 138 NO C 2 2 2 RFZ=2.3 TFZ=8.6
63 123 NO C 2 2 2 RFZ=2.5 TFZ=8.3
64 122 NO C 2 2 2 RFZ=2.5 TFZ=8.2
65 116 NO C 2 2 2 RFZ=2.6 TFZ=8.4
66 118 NO C 2 2 2 RFZ=2.4 TFZ=8.0
67 131 NO C 2 2 2 RFZ=2.4 TFZ=8.3
68 96 NO C 2 2 2 RFZ=2.4 TFZ=8.4
69 98 NO C 2 2 2 RFZ=2.4 TFZ=8.0
70 198 NO C 2 2 2 RFZ=2.5 TFZ=8.6
71 137 NO C 2 2 2 RFZ=2.4 TFZ=8.9
72 110 NO C 2 2 2 RFZ=2.5 TFZ=8.2
73 70 NO C 2 2 2 RFZ=2.4 TFZ=8.4
74 128 NO C 2 2 2 RFZ=2.4 TFZ=8.3
75 87 NO C 2 2 2 RFZ=2.4 TFZ=8.4
76 143 NO C 2 2 2 RFZ=2.5 TFZ=8.2
77 170 NO C 2 2 2 RFZ=2.4 TFZ=8.8
78 170 NO C 2 2 2 RFZ=2.3 TFZ=8.5
79 74 NO C 2 2 2 RFZ=2.7 TFZ=8.2
80 150 NO C 2 2 2 RFZ=2.5 TFZ=8.2
81 71 NO C 2 2 2 RFZ=2.5 TFZ=8.2
82 108 NO C 2 2 2 RFZ=2.5 TFZ=8.1
83 206 NO C 2 2 2 RFZ=2.4 TFZ=8.4
84 114 NO C 2 2 2 RFZ=2.4 TFZ=8.1
85 182 NO C 2 2 2 RFZ=2.4 TFZ=8.2
86 143 NO C 2 2 2 RFZ=2.6 TFZ=8.0
87 92 NO C 2 2 2 RFZ=2.3 TFZ=8.0
88 174 NO C 2 2 2 RFZ=2.4 TFZ=8.5
89 185 NO C 2 2 2 RFZ=2.3 TFZ=8.2
90 111 NO C 2 2 2 RFZ=2.6 TFZ=8.2
91 182 NO C 2 2 2 RFZ=2.5 TFZ=8.3
92 188 NO C 2 2 2 RFZ=2.3 TFZ=8.0
93 158 NO C 2 2 2 RFZ=2.3 TFZ=8.0
94 164 NO C 2 2 2 RFZ=2.4 TFZ=8.6
95 155 NO C 2 2 2 RFZ=2.4 TFZ=8.0
96 130 NO C 2 2 2 RFZ=2.3 TFZ=8.2
97 148 NO C 2 2 2 RFZ=2.4 TFZ=9.0
98 190 NO C 2 2 2 RFZ=2.4 TFZ=8.0
99 147 NO C 2 2 2 RFZ=2.4 TFZ=8.2
100 38 NO C 2 2 21 RFZ=2.7 TFZ=8.5
101 120 NO C 2 2 2 RFZ=2.4 TFZ=8.2
102 133 NO C 2 2 2 RFZ=2.3 TFZ=8.4
103 141 NO C 2 2 2 RFZ=2.4 TFZ=8.7
104 166 NO C 2 2 2 RFZ=2.3 TFZ=8.3
105 88 NO C 2 2 2 RFZ=2.4 TFZ=8.1
106 55 NO C 2 2 21 RFZ=2.4 TFZ=9.9
107 111 NO C 2 2 2 RFZ=2.5 TFZ=8.1
108 61 NO C 2 2 21 RFZ=2.4 TFZ=9.5
109 159 NO C 2 2 2 RFZ=2.4 TFZ=8.4
110 189 NO C 2 2 2 RFZ=2.4 TFZ=8.2
111 37 NO C 2 2 21 RFZ=2.4 TFZ=9.3
112 205 NO C 2 2 2 RFZ=2.4 TFZ=8.6
113 37 NO C 2 2 21 RFZ=2.4 TFZ=9.0
114 37 NO C 2 2 21 RFZ=2.4 TFZ=8.9
115 35 NO C 2 2 21 RFZ=2.4 TFZ=8.6
116 36 NO C 2 2 21 RFZ=2.4 TFZ=8.6
117 59 NO C 2 2 21 RFZ=2.4 TFZ=8.5
118 57 NO C 2 2 21 RFZ=2.4 TFZ=8.4
119 55 NO C 2 2 21 RFZ=2.4 TFZ=8.5
120 59 NO C 2 2 21 RFZ=2.4 TFZ=8.4
121 35 NO C 2 2 21 RFZ=2.4 TFZ=8.2
122 37 NO C 2 2 21 RFZ=2.4 TFZ=8.1
123 37 NO C 2 2 21 RFZ=2.4 TFZ=8.4
124 37 NO C 2 2 21 RFZ=2.4 TFZ=8.1
125 56 NO C 2 2 21 RFZ=2.5 TFZ=8.0
126 59 NO C 2 2 21 RFZ=2.4 TFZ=8.2
127 37 NO C 2 2 21 RFZ=2.4 TFZ=8.0
128 51 NO C 2 2 21 RFZ=2.4 TFZ=8.2
129 69 NO C 2 2 21 RFZ=2.3 TFZ=8.0
0 accepted of 129 solutions
Dataset B
Packing Table
-------------
Solutions accepted if total number of clashes <= 5% of trace atoms
i.e. total number of clashes <= 5
AND if number of clashes <= 5% of trace atoms for each ensemble
i.e. ensemble1: number of clashes <= 5
# # #Clash Packs SpaceGroup Annotation
1 136 NO I 41 2 2 RFZ=2.6 TFZ=12.7
2 136 NO I 41 2 2 RFZ=2.6 TFZ=12.2
3 179 NO I 41 2 2 RFZ=2.6 TFZ=11.2
4 184 NO I 41 2 2 RFZ=2.6 TFZ=10.6
5 133 NO I 41 2 2 RFZ=2.8 TFZ=9.2
6 109 NO I 41 2 2 RFZ=2.8 TFZ=10.9
7 111 NO I 41 2 2 RFZ=2.8 TFZ=10.7
8 153 NO I 41 2 2 RFZ=2.8 TFZ=8.0
9 >6 NO I 41 2 2 RFZ=2.8 TFZ=7.8
10 137 NO I 41 2 2 RFZ=2.8 TFZ=9.0
11 169 NO I 41 2 2 RFZ=2.8 TFZ=9.8
12 189 NO I 41 2 2 RFZ=2.6 TFZ=9.6
13 184 NO I 41 2 2 RFZ=2.8 TFZ=9.7
14 208 NO I 41 2 2 RFZ=2.5 TFZ=9.0
15 117 NO I 41 2 2 RFZ=2.6 TFZ=8.8
16 138 NO I 41 2 2 RFZ=2.6 TFZ=8.5
17 194 NO I 41 2 2 RFZ=3.2 TFZ=8.1
18 206 NO I 41 2 2 RFZ=2.5 TFZ=8.9
19 190 NO I 41 2 2 RFZ=2.7 TFZ=8.1
20 >6 NO I 41 2 2 RFZ=2.8 TFZ=7.4
21 66 NO I 41 2 2 RFZ=2.8 TFZ=8.4
22 >6 NO I 41 2 2 RFZ=3.2 TFZ=7.7
23 185 NO I 41 2 2 RFZ=2.6 TFZ=9.0
24 >6 NO I 41 2 2 RFZ=3.2 TFZ=7.6
25 97 NO I 41 2 2 RFZ=2.6 TFZ=8.2
26 131 NO I 41 2 2 RFZ=2.8 TFZ=9.0
27 180 NO I 41 2 2 RFZ=2.7 TFZ=8.7
28 81 NO I 41 2 2 RFZ=2.6 TFZ=8.2
29 194 NO I 41 2 2 RFZ=2.5 TFZ=8.5
30 135 NO I 41 2 2 RFZ=2.8 TFZ=9.0
31 113 NO I 41 2 2 RFZ=2.6 TFZ=8.1
32 188 NO I 41 2 2 RFZ=2.5 TFZ=8.7
33 174 NO I 41 2 2 RFZ=2.7 TFZ=8.5
34 168 NO I 41 2 2 RFZ=2.6 TFZ=8.4
35 141 NO I 41 2 2 RFZ=2.8 TFZ=8.0
36 188 NO I 41 2 2 RFZ=2.7 TFZ=8.6
37 139 NO I 41 2 2 RFZ=2.6 TFZ=8.3
38 112 NO I 41 2 2 RFZ=2.7 TFZ=8.3
39 183 NO I 41 2 2 RFZ=2.8 TFZ=8.6
40 42 NO I 41 2 2 RFZ=2.6 TFZ=8.3
41 149 NO I 41 2 2 RFZ=2.7 TFZ=8.4
42 188 NO I 41 2 2 RFZ=2.7 TFZ=8.5
43 128 NO I 41 2 2 RFZ=2.4 TFZ=8.1
44 142 NO I 41 2 2 RFZ=2.4 TFZ=8.3
45 151 NO I 41 2 2 RFZ=2.7 TFZ=8.2
46 171 NO I 41 2 2 RFZ=2.6 TFZ=8.3
47 154 NO I 41 2 2 RFZ=2.5 TFZ=8.2
48 180 NO I 41 2 2 RFZ=2.8 TFZ=8.6
49 139 NO I 41 2 2 RFZ=2.4 TFZ=8.1
50 197 NO I 41 2 2 RFZ=2.4 TFZ=8.1
51 181 NO I 41 2 2 RFZ=2.8 TFZ=8.0
52 106 NO I 41 2 2 RFZ=2.8 TFZ=8.2
53 197 NO I 41 2 2 RFZ=2.4 TFZ=8.3
54 98 NO I 41 2 2 RFZ=2.8 TFZ=8.1
55 125 NO I 41 2 2 RFZ=2.5 TFZ=8.1
56 199 NO I 41 2 2 RFZ=2.5 TFZ=8.1
0 accepted of 56 solutions
This protein is a single IgV domain. I have removed all loops, leaving behind
just the beta-strands. Although this appears to place a single copies, searches
for further copies fails despite an increase in the TFZ score;
WARNINGS
--------
$TEXT:Warning: $$ Baubles Markup $$
-------------------------------------------------------------------------------------
Solutions with Z-scores greater than 12.0 (the threshold indicating a definite
solution) were rejected for failing packing test
#3 TFZ=12.0 PAK=33
#9 TFZ=12.7 PAK=61
-------------------------------------------------------------------------------------
$$
$TEXT:Warning: $$ Baubles Markup $$
-------------------------------------------------------------------------------------
Solutions with Z-scores greater than 12.2 (the threshold indicating a definite
solution) were rejected for failing packing test
#1 TFZ=16.3 PAK=67
#2 TFZ=16.1 PAK=38
#3 TFZ=14.8 PAK=37
#4 TFZ=13.9 PAK=64
#5 TFZ=12.3 PAK=85
#6 TFZ=12.4 PAK=67
#7 TFZ=12.6 PAK=65
-------------------------------------------------------------------------------------
$$
So three things
1) Is this working?
2) Do I need to fragment the protein differently? As in remove some strands
instead of loops?
or
3) Something else?
I am currently shooting crystals looking for slightly higher datasets, so If
you have any suggestions, please let me know.
Thanks and enjoy the weekend.
Dan
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