Hi Tiantian,
You say you have a 'co-crystal' of your protein with the magic triangle, but how do you really know that I3C is there? The fact that you put it into the crystallization drop doesn't necessarily mean that it made it into the crystal. In fact, based on the <d''/sig> output of shelxc that you provided in your original email, it seems to me that your data have very little anomalous signal. <d''/sig> can be taken as a measure of the strength of the anomalous signal, and it typically starts at high values in the lowest resolution shells and then falls off asymptotically to a value of ~0.8 at high resolution. Therefore, 0.8 can be taken as a general indicator of 'no anomalous signal." Your <d''/sig> values are relatively constant at about 0.7-1.0 across the entire resolution range of your data, and therefore I would say that you have little or no anomalous signal in the data. I therefore wonder whether the I3C is actually bound at all. In my personal experience, I would be very surprised indeed if this data set were to give a successful SAD solution. The lack of useful anomalous signal is reflected in the fact that your CCall/CCweak values are so low, indicating to me that, unfortunately, the phase problem is not yet successfully solved. Good luck in your future phasing trials! Matthew --- Matthew J. Whitley, Ph.D. Research Instructor Department of Pharmacology & Chemical Biology University of Pittsburgh School of Medicine ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of CCP4BB automatic digest system <lists...@jiscmail.ac.uk> Sent: Thursday, April 25, 2019 7:01 PM To: CCP4BB@JISCMAIL.AC.UK Subject: CCP4BB Digest - 24 Apr 2019 to 25 Apr 2019 (#2019-124) Date: Thu, 25 Apr 2019 11:05:05 -0400 From: ChenTiantian <chentiantian2...@gmail.com> Subject: weak anomalous phasing (magic triangle I3C) Dear all, I'm working on a 18kD protein, the secondary structure prediction says most of the structure is beta sheets, trying to solve the structure with SAD. Heavy atom soaking gives several datasets with I, W, Au, range from 2.7~3.7A, however, the anomalous signal is pretty weak, I couldn't find a reasonable solution. We got a co-crystal dataset with the magic triangle I3C, extends to around 2.5A, this is the best data we got so far. shelxc gives me the following result: Resl. Inf. 12.59 7.75 5.84 4.77 4.08 3.59 3.22 2.94 2.70 2.51 2.35 N(data) 79 257 429 635 811 1010 1235 1384 1698 1555 1954 Chi-sq 0.69 0.63 0.60 0.67 0.61 0.88 1.05 1.02 0.80 0.55 0.42 <I/sig> 79.4 34.1 30.3 32.2 31.8 26.6 21.1 14.6 8.3 3.9 2.4 %Complete 94.0 98.1 97.5 99.5 99.4 99.0 99.7 100.0 99.9 85.4 96.1 Multipl. 4.0 4.5 3.9 4.5 4.7 4.2 4.4 4.8 5.0 4.3 4.4 R(pim)% 2.27 1.72 2.29 2.05 2.02 2.62 3.51 4.84 7.90 14.43 22.78 Ranom% 6.49 3.68 5.19 4.29 4.27 6.35 9.50 12.97 20.90 33.58 52.21 <d"/sig> 0.73 0.80 1.08 0.85 0.95 1.03 1.00 0.91 0.85 0.78 0.70 CC(1/2) 5.1 41.7 68.8 38.1 42.7 49.9 49.9 25.5 24.9 13.3 -4.7 then I tried shelxd with different heavy atom sites number and resolution cut, the best CC I got is CC/CCweak: 24.75/7.69, and I can identify a triangle, (length: 6.5/6.5/5.0A), however, both shelxe and autosol didn't end up with a promising result. [image: image.png] It would be great if anyone can give me some suggestions. Thank you in advance! -- Tiantian ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
