Hi James, My initial thought is that a 3-sigma bond length deviation is significant. When we make an experiment and observe something that doesn’t correspond to what we expect, it could be an error, or it could be that we found the thread for a new discovery.
If the experimental data supports that deviation, I would look at the experimental data carefully because that can show you a surprise. Maybe it is a different bond than you were expecting? Maybe a different geometry? I assume you are talking about a protein crystal structure that was collected at the synchrotron, but you should analyze the data and consider what is the resolution of your data? What is the completeness? What is the B-factor? How did you refine those bonds? If you have low resolution you might have more variability, but we typically impose more restrictions during refinement and might not observe those variations. When you represent your crystal structure by a model, you have to consider that in a crystal you have an average of structures in the crystal lattice, and an average in time, where radiation damage is also occurring . If the experiment is well done, the data might point you to something relevant. Maybe the atoms you are considering C-C bond are not what you thought and therefore the bond is different. One example can be observed in interactions of proteins with metals, where initially we refine the model thinking we have one metal and it shows a mixture of metals, or a completely different one. I know you will do a fluorescence scan in your MAD beamline to sort it out 😊 Best wishes, Joao -----Original Message----- From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of James Holton Sent: Tuesday, November 8, 2022 5:22 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [EXTERNAL] [ccp4bb] outliers OK, so lets suppose there is this bond in your structure that is stretched a bit. Is that for real? Or just a random fluke? Let's say for example its a CA-CB bond that is supposed to be 1.529 A long, but in your model its 1.579 A. This is 0.05 A too long. Doesn't seem like much, right? But the "sigma" given to such a bond in our geometry libraries is 0.016 A. These sigmas are typically derived from a database of observed bonds of similar type found in highly accurate structures, like small molecules. So, that makes this a 3-sigma outlier. Assuming the distribution of deviations is Gaussian, that's a pretty unlikely thing to happen. You expect 3-sigma deviates to appear less than 0.3% of the time. So, is that significant? But, then again, there are lots of other bonds in the structure. Lets say there are 1000. With that many samplings from a Gaussian distribution you generally expect to see a 3-sigma deviate at least once. That is, do an "experiment" where you pick 1000 Gaussian-random numbers from a distribution with a standard deviation of 1.0. Then, look for the maximum over all 1000 trials. Is that one > 3 sigma? It probably is. If you do this "experiment" millions of times it turns out seeing at least one 3-sigma deviate in 1000 tries is very common. Specifically, about 93% of the time. It is rare indeed to have every member of a 1000-deviate set all lie within 3 sigmas. So, we have gone from one 3-sigma deviate being highly unlikely to being a virtual certainty if you look at enough samples. So, my question is: is a 3-sigma deviate significant? Is it significant only if you have one bond in the structure? What about angles? What if you have 500 bonds and 500 angles? Do they count as 1000 deviates together? Or separately? I'm sure the more mathematically inclined out there will have some intelligent answers for the rest of us, however, if you are not a mathematician, how about a vote? Is a 3-sigma bond length deviation significant? Or not? Looking forward to both kinds of responses, -James Holton MAD Scientist ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!H9nueQsQ!59F_VEEPv4VzGZgCp3sN73Rj4vKyZBcIOY9TwFRyr0U47aUiTqIIkUg_5ib8dT46tiKEAgQxf378QBG7$ This message was issued to members of https://urldefense.com/v3/__http://www.jiscmail.ac.uk/CCP4BB__;!!H9nueQsQ!59F_VEEPv4VzGZgCp3sN73Rj4vKyZBcIOY9TwFRyr0U47aUiTqIIkUg_5ib8dT46tiKEAgQxf28joQL8$ , a mailing list hosted by https://urldefense.com/v3/__http://www.jiscmail.ac.uk__;!!H9nueQsQ!59F_VEEPv4VzGZgCp3sN73Rj4vKyZBcIOY9TwFRyr0U47aUiTqIIkUg_5ib8dT46tiKEAgQxfwxM1QmH$ , terms & conditions are available at https://urldefense.com/v3/__https://www.jiscmail.ac.uk/policyandsecurity/__;!!H9nueQsQ!59F_VEEPv4VzGZgCp3sN73Rj4vKyZBcIOY9TwFRyr0U47aUiTqIIkUg_5ib8dT46tiKEAgQxf1Mbwaqi$ ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
