Hello, the statistics all look good apart from the R-merge and R-meas. It might be worth looking at the processing again in case it can be improved. I assume you mean rms rather than A when you say the difference density only disappears at 6 A and, if so, it must be a strong feature. Does the fragment you have refined make chemical sense, either as a possible hydrolysis product, impurity or distinct binding group? Sorry, not much helpful advice here.
On 20 Dec 2019 04:57, Katherine Lim <katherine....@research.uwa.edu.au> wrote:
Hi all,I apologise in advance for the long post. I am working on solving a structure that looks like it could have a ligand bound in the active site. My data was obtained from a crystal of just the soluble domain of my protein that had been soaked overnight in the ligand solution. The apo crystal structure is already known and so I have solved my structure using phaser MR. I have attached the Aimless report output of my structure at the end of this email. The current R values I have after refinement and adding in all the waters are Rfree: 0.2413 and Rwork: 0.1897. I can clearly see green density that is much larger (only disappears when I contour the Fo-Fc map to about 6 A) than in my control crystal that had been soaked in the same concentration of just solvent (I had used DMF).I am struggling to add in my ligand as it doesn't seem like the entire ligand can fit in the green density. We think it may be because we have only used the soluble domain and so the ligand isn't held very securely since the transmembrane domain is missing. I have been trying to fit in smaller sections of it and doing an occupancy refinement. So far I have been able to get part of the ligand in with an occupancy of about 0.6 but after the refinement run, phenix.refine seems to move this part of the ligand slightly out of the area where I had tried to fit it into the green density. Interestingly, there isn't a big red density in the area that this ligand section has moved to. I would appreciate any advice on how I should proceed with trying to figure out if I have tried the correct section of the ligand and the kind of refinement settings to use with a weak binder.
Space Group P212121 Unit cell abc 84.76, 89.84, 91.55 unit cell alpha beta gamma 90, 90, 90 OVERALL LOW RES HIGH RES Low res limit 45.78 45.78 1.94 High res limit 1.9 9.11 1.9 Rmerge 0.234 0.052 1.684 Rmeas 0.244 0.054 1.768 Rpim 0.069 0.016 0.527 Total # observations 663073 6282 36851 Total # unique 55174 579 3359 I/sigma 7.5 27.9 1.4 CC ½ 0.997 0.999 0.747 Completeness % 99 98.7 94.7 Multiplicity 12 10.8 11 Katherine Lim
PhD Candidate
School of Biomedical Sciences; School of Molecular Sciences
Marshall Centre for Infectious Disease Research and Training
The University of Western Australia
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