Re: [ccp4bb] AW: Differences in a homodimer protein

Thank you Eleanor, I did the PISA analysis and one of the "high B" chains in the region of my metal had a BSA ~ 10% lower than that of the "Low B" chain. I don't know if that is a significant difference. Best Denis From: Eleanor Dodson

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Re: [ccp4bb] AW: Differences in a homodimer protein

I would submit the coordinates to PISA to analyse the buried surface area for each momnomer and see if there are differences. It is pretty common that some copies have much lower B values and therefore are better defined.. Eleanor On 29 November 2017 at 17:15, Denis Rousseau

Re: [ccp4bb] AW: Differences in a homodimer protein

I want to thank everyone on the BB for their comments about the differences in the homodimeric protein. I had done a superposition of the structures and found no differences that could account for the differences in the water occupancy I observed. However, I had not compared the B factors which

Re: [ccp4bb] AW: Differences in a homodimer protein

I have seen this in MnSOD. We had a tetramer in the ASU and each active site had different ligands in our peroxide soak. I assumed the crystal lattice can influence these things or it is inappropriate metal incorporation. I would highly recommend doing ICP-MS on a dissolved crystal and on your

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Re: [ccp4bb] looking for a link between diffraction resolution and order within the crystal

Thank you everyone for your contributions that help me understand more. Let me try to rephrase my initial post: Say that I have diffraction up to 6A resolution, I would say that my crystal is decently ordered (see the glass half full), enough for observing repeating units that do not fluctuate

Re: [ccp4bb] Differences in a homodimer protein

Denis, Others may have addressed this, but you have not mentioned your refinement conditions. At 2.4 Å, are you using what and how early in the refinement is your work? NCS restraints, group B refinement, individual B refinement, etc. A little more information would help the BB readers

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That depends on the quality of your data and your model! I play with refinement and rebuilding - check indicators v resolution., etc etc (I look at the v plot from REFMAC - can show up problems with low resolution data. Eleanor On 29 November 2017 at 12:46, YUVARAJ I

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Dear all Iodine gave a good anomalous signal at copper k-alpha wavelength. Thank you everyone for your good suggestions. I could build the model and refine it and bring the R-factor/ R-free 0.214/ 0.247 at the resolution of 1.6A (with the previous data set without anomalous signal,

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[ccp4bb] Microheterogeneity and LINKs to Symmetry objects

Hello I have two questions relating to the same protein build. I am struggling with an interesting case of a protein structure for which we have chosen to build it with microheterogeneity. In summary, we have an all alpha helical highly repetitive solenoidal RNA binding protein. In our

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