Thank you all for responses. I have added my reply below.
On 26 October 2016 at 17:02, Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote:
> Are your 3 crystals isomorphous, and do they all refine well?
Yes, all C2221 crystal datasets refine to ~ 19/23 %
> I guess you struck lucky with DS3 - as suggested it could be a different
> soaking, different crystal size, etc, etc..
>
> If isomorphous I would compare all 3 structures in COOT and look for subtle
> differences..
We have.
> Your C222 and C2221 cells are obviously related but have slightly different
> cell volumes so cannot be exactly the same. Do you have any
> non-crystallographic translation - that can confuse the assignment of 2_1
On 26 October 2016 at 16:47, Tristan Croll <ti...@cam.ac.uk> wrote:
> Are these three crystals in order of harvesting (with different soaking
> times)? How big is your ligand. How accessible is the binding pocket (and is
> there a clear difference in accessibility between chains)?
>
> T
>
Three separate drops; but crystal sizes for C2221 varied 100 -150
microns. Even the other crystal form C222, was from different drop
(same crystallisation condition)
Binding pocket is accessible even in unbound chains. Let me clarify.
There are 4 chains; 4 binding sites. Two of the binding pockets
located close to one another; and another 2 are far away from any
other (even in packing). The sites are close to one another are always
unoccupied but the sites that are lonely, always have occupied.
I asked this as I wonder if referees might ask _why_ in some chains
COA is unbound.
On 26 October 2016 at 17:11, Zbyszek Otwinowski <zbys...@work.swmed.edu> wrote:
> What is the height of non-origin Patterson function peak for your data sets?
>
> have pseudotranslational symmetry that can be detected by calculating the
> Patterson function. You should have strong reflections with all indexes
> even or odd, and other reflections being weaker. What is the spot shape of
> these weaker spots?
>
> In case of pseudotranslational symmetry, MR can produce a pseudosolution
> related to the correct one by pseudotranslational symmetry vector.
> Translate your C2221 solution by {0, 0.5, 0.5} and try refining again.
>
I ran peakmax within molrep/ccp4i:
List of peaks in order of location -C222
==================================
Peaks related by symmetry are assigned the same site number
Count Site Height Grid Fractional coordinates
Orthogonal coordinates
WARNING: delta Rho too small for peak determination at 263 52 9,
delrho values 0.6313E-03 0.0000E+00
WARNING: delta Rho too small for peak determination at 263 60 9,
delrho values 0.6313E-03 0.0000E+00
***** 8000 peaks found, check value of RMN
NOP highest peaks are selected from these
1 1 100.00 0 0 0 0.0000 0.0000 0.0000
0.00 0.00 0.00
2 2 14.21 23 0 0 0.2059 0.0000 0.0000
30.27 0.00 0.00
3 3 13.65 30 0 0 0.2680 0.0000 0.0000
39.40 0.00 0.00
4 4 14.39 51 0 0 0.4548 0.0000 0.0000
66.87 0.00 0.00
5 5 14.13 56 0 0 0.5000 0.0000 0.0000
73.53 0.00 0.00
6 4 14.39 61 0 0 0.5452 0.0000 0.0000
80.18 0.00 0.00
7 3 13.65 82 0 0 0.7320 0.0000 0.0000
107.65 0.00 0.00
8 2 14.21 89 0 0 0.7941 0.0000 0.0000
116.78 0.00 0.00
9 1 63.04 111 0 0 0.9911 0.0000 0.0000
145.74 0.00 0.00
10 6 14.31 36 1 0 0.3201 0.0025 0.0000
47.07 0.90 0.00
11 6 14.31 76 1 0 0.6799 0.0025 0.0000
99.98 0.90 0.00
12 7 13.93 41 2 0 0.3670 0.0076 0.0000
53.96 2.70 0.00
13 8 14.25 48 2 0 0.4283 0.0093 0.0000
62.98 3.28 0.00
14 8 14.25 64 2 0 0.5717 0.0093 0.0000
84.07 3.28 0.00
15 7 13.93 71 2 0 0.6330 0.0076 0.0000
93.09 2.70 0.00
16 9 14.03 10 3 0 0.0908 0.0129 0.0000
13.36 4.57 0.00
17 10 14.78 16 3 0 0.1439 0.0096 0.0000
21.16 3.39 0.00
18 11 14.15 29 3 0 0.2597 0.0129 0.0000
38.19 4.56 0.00
19 12 13.83 33 3 0 0.2915 0.0111 0.0000
42.86 3.93 0.00
20 12 13.83 79 3 0 0.7085 0.0111 0.0000
104.19 3.93 0.00
21 11 14.15 83 3 0 0.7403 0.0129 0.0000
108.86 4.56 0.00
22 10 14.78 96 3 0 0.8561 0.0096 0.0000
125.89 3.39 0.00
23 9 14.03 102 3 0 0.9092 0.0129 0.0000
133.69 4.57 0.00
24 13 14.22 25 4 0 0.2259 0.0138 0.0000
33.22 4.88 0.00
25 14 15.02 56 4 0 0.5000 0.0158 0.0000
73.53 5.60 0.00
26 13 14.22 87 4 0 0.7741 0.0138 0.0000
113.83 4.88 0.00
27 15 13.95 19 5 0 0.1734 0.0204 0.0000
25.49 7.22 0.00
28 15 13.95 93 5 0 0.8266 0.0204 0.0000
121.56 7.22 0.00
29 16 14.01 36 6 0 0.3216 0.0227 0.0000
47.28 8.03 0.00
List of peaks in order of location - C2221
==================================
Peaks related by symmetry are assigned the same site number
Count Site Height Grid Fractional coordinates
Orthogonal coordinates
WARNING: delta Rho too small for peak determination at 0 38 3,
delrho values 0.8545E-03 0.0000E+00
WARNING: delta Rho too small for peak determination at 0 122 3,
delrho values 0.8545E-03 0.0000E+00
WARNING: delta Rho too small for peak determination at 130 42 3,
delrho values 0.8545E-03 0.0000E+00
WARNING: delta Rho too small for peak determination at 130 118 3,
delrho values 0.8545E-03 0.0000E+00
***** 8000 peaks found, check value of RMN
NOP highest peaks are selected from these
1 1 100.00 0 0 0 0.0000 0.0000 0.0000
0.00 0.00 0.00
2 2 14.37 11 0 0 0.0680 0.0000 0.0000
14.72 0.00 0.00
3 3 15.04 13 0 0 0.0843 0.0000 0.0000
18.26 0.00 0.00
4 4 14.74 17 0 0 0.1056 0.0000 0.0000
22.88 0.00 0.00
5 5 15.00 24 0 0 0.1525 0.0000 0.0000
33.03 0.00 0.00
6 6 14.30 29 0 0 0.1805 0.0000 0.0000
39.08 0.00 0.00
7 7 14.25 37 0 0 0.2295 0.0000 0.0000
49.70 0.00 0.00
8 8 14.25 49 0 0 0.3051 0.0000 0.0000
66.08 0.00 0.00
9 9 14.65 68 0 0 0.4238 0.0000 0.0000
91.78 0.00 0.00
10 10 14.13 72 0 0 0.4529 0.0000 0.0000
98.08 0.00 0.00
11 11 14.79 80 0 0 0.5000 0.0000 0.0000
108.28 0.00 0.00
12 10 14.13 88 0 0 0.5471 0.0000 0.0000
118.48 0.00 0.00
13 9 14.65 92 0 0 0.5762 0.0000 0.0000
124.79 0.00 0.00
14 8 14.25 111 0 0 0.6949 0.0000 0.0000
150.49 0.00 0.00
15 7 14.25 123 0 0 0.7705 0.0000 0.0000
166.87 0.00 0.00
16 6 14.30 131 0 0 0.8195 0.0000 0.0000
177.48 0.00 0.00
17 5 15.00 136 0 0 0.8475 0.0000 0.0000
183.53 0.00 0.00
18 4 14.74 143 0 0 0.8944 0.0000 0.0000
193.69 0.00 0.00
19 3 15.04 147 0 0 0.9157 0.0000 0.0000
198.30 0.00 0.00
20 2 14.37 149 0 0 0.9320 0.0000 0.0000
201.84 0.00 0.00
21 1 64.98 159 0 0 0.9937 0.0000 0.0000
215.21 0.00 0.00
22 12 14.43 52 2 0 0.3239 0.0083 0.0000
70.15 2.87 0.00
23 12 14.43 108 2 0 0.6761 0.0083 0.0000
146.41 2.87 0.00
24 13 14.62 46 4 0 0.2891 0.0140 0.0000
62.60 4.85 0.00
25 14 14.36 55 4 0 0.3407 0.0161 0.0000
73.79 5.55 0.00
26 15 14.25 72 4 0 0.4483 0.0153 0.0000
97.09 5.28 0.00
27 15 14.25 88 4 0 0.5517 0.0153 0.0000
119.48 5.28 0.00
28 14 14.36 105 4 0 0.6593 0.0161 0.0000
142.78 5.55 0.00
29 13 14.62 114 4 0 0.7109 0.0140 0.0000
153.96 4.85 0.00
30 16 14.15 0 5 0 0.0000 0.0182 0.0000
0.00 6.29 0.00
31 17 15.41 12 5 0 0.0779 0.0200 0.0000
16.87 6.93 0.00
32 18 14.40 30 5 0 0.1874 0.0198 0.0000
40.59 6.85 0.00
33 19 14.62 63 5 0 0.3961 0.0180 0.0000
85.77 6.22 0.00
>
>
>
> There are 2 aspects to your enquiry:
>
> 1- The different number of ligands in your structure could be easily
> sorted out by a longer soak. You don’t have to stick with 1 minute soak. A
> day or longer (I’ve heard of a case in which the soak went on for 30 days),
> would fill up as many sites as can take your ligand. Of course, the soak
> would have to be neutral to the crystal, i.e. won’t cause any damage.
The crystals crack on soak very easily. So I had to fish them ASAP.
