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It looks a brilliant MR solution.. Do you know how you expect the A/B sets to pack? This was always a problem with heamoglobin where the A & B chains are very similar ad form a tetramer, but we would group the solutions iinto sensible tetramers (PISA will do that for you) and either set those residues which were different to ALA then try to use the density to check or fit the known teramer both ways so that one had the correct A/B match and the other did not, then let the refinement choose which fit was better. Eleanor On 5 February 2015 at 16:03, Dom Bellini <[log in to unmask]> wrote: > Did you try ShelxE autotrace? At that resolution it should work nicely, or > at least be able to distinguish between the two sequences. > > D > > -----Original Message----- > From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of > Keller, Jacob > Sent: 05 February 2015 15:49 > To: ccp4bb > Subject: Re: [ccp4bb] Resolve Domain Sequence Ambiguities > > Sorry--should have included a bit more info: > > A huge caveat: data is tetartohedrally twinned, which makes everything an > issue. But, I have managed to get Rfree down to ~32% in refmac with > intensity-based twin refinement. I know--R's with de-twinning are illusory, > but I still think it's solved, since I also can see anomalous signal in > partial-model LLG maps from phaser at places predicted by the structure > (and I don't think that anomalous info could be encoded in the MR phases > (can it?)). So, that was a nice confirmatory moment... > > Resolution is good, but cut off by detector limit on home system (set at > max resolution w/o 2theta) > > N 1/d^2 Dmid CCanom Nanom RCRanom CC1/2 NCC1/2 Rsplit > CCfit CCanomfit $$ $$ > 1 0.0061 12.82 -0.018 938 0.982 0.998 989 0.028 > 1.000 0.001 > 2 0.0182 7.40 0.026 1831 1.026 0.998 1880 0.027 > 1.000 0.006 > 3 0.0304 5.73 0.062 2334 1.064 0.995 2385 0.032 > 1.000 0.010 > 4 0.0426 4.85 0.048 2806 1.049 0.995 2881 0.033 > 1.000 0.014 > 5 0.0547 4.27 0.036 3164 1.036 0.995 3243 0.034 > 1.000 0.019 > 6 0.0669 3.87 0.025 3524 1.026 0.994 3606 0.035 > 1.000 0.023 > 7 0.0791 3.56 0.011 3758 1.011 0.993 3873 0.038 > 1.000 0.027 > 8 0.0912 3.31 0.021 4111 1.021 0.993 4206 0.041 > 0.999 0.032 > 9 0.1034 3.11 -0.003 4340 0.997 0.991 4441 0.044 > 0.999 0.036 > 10 0.1155 2.94 -0.040 4602 0.961 0.989 4724 0.049 > 0.999 0.040 > 11 0.1277 2.80 0.050 4864 1.051 0.991 4968 0.048 > 0.999 0.045 > 12 0.1399 2.67 0.051 4996 1.052 0.988 5121 0.052 > 0.998 0.049 > 13 0.1520 2.56 0.073 5348 1.076 0.988 5469 0.053 > 0.997 0.053 > 14 0.1642 2.47 -0.009 5486 0.991 0.987 5611 0.057 > 0.996 0.058 > 15 0.1764 2.38 0.032 5698 1.032 0.985 5827 0.061 > 0.995 0.062 > 16 0.1885 2.30 0.091 5945 1.095 0.985 6067 0.063 > 0.993 0.066 > 17 0.2007 2.23 0.038 6002 1.039 0.985 6118 0.064 > 0.991 0.070 > 18 0.2128 2.17 0.086 6331 1.089 0.983 6445 0.068 > 0.987 0.075 > 19 0.2250 2.11 0.075 6411 1.078 0.983 6556 0.070 > 0.983 0.079 > 20 0.2372 2.05 0.097 6608 1.102 0.983 6756 0.070 > 0.977 0.083 > 21 0.2493 2.00 0.141 6712 1.152 0.981 6880 0.078 > 0.968 0.088 > 22 0.2615 1.96 0.104 6556 1.110 0.974 7126 0.093 > 0.957 0.092 > 23 0.2737 1.91 0.141 5595 1.152 0.953 7054 0.121 > 0.943 0.096 > 24 0.2858 1.87 0.149 4659 1.160 0.936 6652 0.151 > 0.923 0.101 > 25 0.2980 1.83 0.125 3630 1.133 0.909 5936 0.184 > 0.898 0.105 > 26 0.3101 1.80 0.138 2640 1.148 0.874 5118 0.219 > 0.866 0.109 > 27 0.3223 1.76 0.111 1793 1.116 0.851 4035 0.250 > 0.825 0.114 > 28 0.3345 1.73 0.040 1040 1.041 0.782 2857 0.305 > 0.776 0.118 > 29 0.3466 1.70 0.094 300 1.097 0.713 1474 0.371 > 0.717 0.122 > 30 0.3588 1.67 - 2 - 0.589 228 0.497 > 0.649 0.127 > $$ > Overall: 0.027 122024 1.027 0.997 138526 0.048 > CCanom Nanom RCRanom CC1/2 NCC1/2 Rsplit > CCfit CCanomfit > > > > MR solution: > > SOLU SET RFZ=3.9 TFZ=7.1 PAK=0 LLG=38 RFZ=3.7 TFZ=8.9 PAK=0 LLG=75 RFZ=4.2 > TFZ=8.2 PAK=0 LLG=40 LLG=160 RFZ=3.2 TFZ=11.2 PAK=0 LLG=249 LLG=262 > RFZ=4.2 > TFZ=9.4 PAK=0 LLG=331 LLG=339 RFZ=4.1 TFZ=11.3 PAK=0 LLG=405 LLG=418 > RFZ=3.9 > TFZ=11.6 PAK=0 LLG=487 LLG=494 RFZ=4.2 TFZ=8.9 PAK=0 LLG=539 LLG=554 > RFZ=3.3 > TFZ=8.6 PAK=0 LLG=612 LLG=638 RFZ=3.1 TFZ=8.7 PAK=0 LLG=679 LLG=691 > RFZ=2.6 > TFZ=12.4 PAK=0 LLG=910 LLG=926 RFZ=3.0 TFZ=9.2 PAK=0 LLG=987 LLG=1001 > RFZ=2.7 > TFZ=9.8 PAK=3 LLG=1018 LLG=1043 RFZ=2.9 TFZ=9.1 PAK=5 LLG=1039 > > > > > > > > > > > > > > > -----Original Message----- > From: [log in to unmask] [mailto:[log in to unmask]] > Sent: Thursday, February 05, 2015 10:28 AM > To: Keller, Jacob; [log in to unmask] > Subject: RE: Resolve Domain Sequence Ambiguities > > Dear Jacob, > > Are you sure your MR solution is correct? What is your resolution? > > Best, > > D > > -----Original Message----- > From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of > Keller, Jacob > Sent: 05 February 2015 15:21 > To: ccp4bb > Subject: [ccp4bb] Resolve Domain Sequence Ambiguities > > Hi All, > > I have 14 identical domains placed in my ASU with reasonable MR scores, > but the problem is that there should really be 7+7 or 8+8 of domains A and > B (which are structurally similar). Can anyone think of a great and easy > way of resolving the ambiguity? > > I was thinking potentially: > > -change one domain to polyAla > -SA omit map of that one > -rebuild/refine > -iterate through all domains, noting scores > > Seems it might be pretty low reliability and a fair amount of work though. > Otherwise, could try to go back to a small SAD signal, use partial model > phases to find HAs, then phase without the model, rebuild from there. Any > thoughts or similar experiences? > > JPK > > > ******************************************* > Jacob Pearson Keller, PhD > Looger Lab/HHMI Janelia Research Campus > 19700 Helix Dr, Ashburn, VA 20147 > email: [log in to unmask] > ******************************************* > > -- > This e-mail and any attachments may contain confidential, copyright and or > privileged material, and are for the use of the intended addressee only. 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