Subject: | | Re: Molecular replacement question |
From: | | Eleanor Dodson <[log in to unmask]> |
Reply-To: | | [log in to unmask][log in to unmask], 8 Sep 2010 22:50:40 -0400763_iso-8859-1 A large amount of hypotheticals can be found in Plasmodium :-)
Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/
On Sep 8, 2010, at 9:29 PM, Ed Pozharski wrote:
> David is absolutely right. There is no design, Jacob, we just > instinctively look for it everywhere because seeking purpose instead of > understanding mechanism conveys advantage to our species. Your > rationale is flawed - just because it is imaginable [...][log in to unmask] |
Date: | | Mon, 13 Sep 2010 16:16:50 +0100 |
Content-Type: | | text/plain |
Parts/Attachments: |
|
|
|
|
Does your model structure form a dimer? Maybe best to search with that
model..
eleanor
Paul Holland wrote:
> Hello fellow crystallographers,
>
> I am trying molecular replacement for a protein crystal dataset that has very high sequence similarity to the search model with several predicted flexible loop regions; however, all attempts at finding a solution have not produce very ideal starting solutions using Phaser and Molrep (CC = 0.3 and Z-score = 5). I am very confident that the unit cell parameters are C2 84.027 120.565 108.272 90.00 104.71 90.00, and there appears to be no evidence of twinning. The Matthews calculation predicts from anywhere from 2-4 monomers in the ASU, and calculation of the SRF in Molrep does not identify any peaks in higher order symmetry except for the expected crystallographic two-fold for C2. Below is the table from the calculated SRF in molrep. Any advice would be greatly appreciated.
>
> # theta phi chi alpha beta gamma Rf Rf/sigma
> Sol_RF 1 0.00 0.00 0.00 0.00 0.00 0.00 870.5 21.59
> Sol_RF 2 58.61 -10.17 180.00 169.83 -117.23 10.17 162.5 4.03
> Sol_RF 3 66.02 -0.00 180.00 180.00 -132.03 0.00 161.1 4.00
> Sol_RF 4 58.42 -9.54 180.00 170.46 -116.85 9.54 159.8 3.96
> Sol_RF 5 149.84 0.00 180.00 -180.00 60.32 0.00 156.0 3.87
> Sol_RF 6 58.96 -5.52 180.00 174.48 -117.91 5.52 151.5 3.76
> Sol_RF 7 65.59 20.95 180.00 20.95 131.18 159.05 143.9 3.57
> Sol_RF 8 90.00 -98.96 180.00 0.00 180.00 17.92 142.9 3.55
> Sol_RF 9 56.53 15.78 180.00 15.78 113.07 164.22 142.0 3.52
> Sol_RF 10 71.10 -19.94 180.00 160.06 -142.20 19.94 141.6 3.51
> Sol_RF 11 71.28 29.78 180.00 29.78 142.55 150.22 140.4 3.48
> Sol_RF 12 65.22 -15.88 180.00 164.12 -130.44 15.88 139.2 3.45
> Sol_RF 13 68.84 -0.00 180.00 180.00 -137.67 0.00 138.0 3.42
> Sol_RF 14 32.51 -180.00 180.00 -180.00 65.02 -0.00 137.9 3.42
> Sol_RF 15 75.02 -28.84 180.00 151.16 -150.04 28.84 134.7 3.34
> Sol_RF 16 71.69 -20.99 180.00 159.01 -143.37 20.99 133.0 3.30
> Sol_RF 17 92.13 101.46 179.93 102.35 -175.74 79.42 130.9 3.25
> Sol_RF 18 107.89 144.73 179.79 145.06 -144.22 35.61 128.8 3.19
> Sol_RF 19 87.45 -78.19 180.00 101.81 -174.90 78.19 128.1 3.18
> Sol_RF 20 38.57 0.69 30.36 102.66 -18.79 -78.71 122.4 3.04
> Sol_RF 21 26.77 174.59 176.58 172.68 53.52 3.49 120.5 2.99
> Sol_RF 22 116.66 178.08 175.14 3.49 126.48 187.32 120.5 2.99
> Sol_RF 23 75.56 -41.35 180.00 138.65 -151.12 41.35 119.8 2.97
> Sol_RF 24 66.12 36.35 180.00 36.35 132.24 143.65 116.6 2.89
> Sol_RF 25 83.87 71.62 180.00 71.62 167.74 108.38 114.7 2.85
> Sol_RF 26 69.24 -12.37 180.00 167.63 -138.48 12.37 112.3 2.79
> Sol_RF 27 59.75 15.26 172.29 7.64 119.07 157.12 112.2 2.78
> Sol_RF 28 120.25 -164.74 172.29 22.88 119.07 172.36 112.2 2.78
> Sol_RF 29 96.68 -70.99 180.00 109.01 -166.63 70.99 110.9 2.75
> Sol_RF 30 63.23 -44.73 180.00 135.27 -126.47 44.73 108.9 2.70
>
> Cheers,
>
> Paul Holland
>
>
|
|
|
|