Re: [ccp4bb] structure with missing density

Dear Deepanshu, Is the primary sequence in the neighbourhood of your missing strands conserved? Perhaps that part differs in your structure relative to the search model. Have you tried omitting the region from MR and rerunning refinement without to see if some new density pops up? If not,

[ccp4bb] structure with missing density

Dear all, I am working on a protein complex. After many efforts, I obtained crystals from one of the refinement screen (which took few weeks to grow) and I got a 3 Å dataset at synchrotron. I scaled the dataset in P21 spacegroup (which is also confirmed by Zanuda and Pointless). There is no

Re: [ccp4bb] Issue with high Rfree (0.25) for a high-resolution dataset (1.05 Ang)

I do think at times the Rfree is a bit of a sacred cow . At one level if the maps look OK not much can be wrong.. Is the Ramachandran plot OK? You dont say what the R factor is but does this mean there is a large difference between the Rfactor and Rfree? If you are using REFMAC look at the plots

[ccp4bb] CCN resend

Folks It seems that 50% of people got an email that was 50% greek. I have tried to remove this by removing formatting. Hope this helps. The second 2018 issue of the CCN is now available at http://phenix-online.org/newsletter/ Articles include · Fitting tips #16 – Vicinal disulfides: Have

Re: [ccp4bb] Issue with high Rfree (0.25) for a high-resolution dataset (1.05 Ang)

Hello, at that resolution, the refinement of anisotropic atomic B-factors is absolutely required, as is the modelisation of alternate conformations for surface residues. Optimize also the weight of different restraints (for exemple on B-factors) in order to get the lowest Rfree. Best Wim

Re: [ccp4bb] Issue with high Rfree (0.25) for a high-resolution dataset (1.05 Ang)

Hi Guto, I would be very cautious with the InnerShell merging statistics as yours. Rmeas in this shell is higher than Rmeas overall, which probably means you have a lot of overloads, (or problems with backstop shadow, which is not so likely on Diamond nowdays). And generally InnerShell Rmerge

Re: [ccp4bb] Issue with high Rfree (0.25) for a high-resolution dataset (1.05 Ang)

Hi Hugo, Perhaps you should play with your refinement strategy. Use a decent number of cycles and a sensible restraint weight (something that gives you rmsZ < 1.0 and good R-factors). Anisotropic B-factors are probably needed and make your model as complete as your maps allow. You could try

[ccp4bb] Computational Crystallography Newsletter

Folks The second 2018 issue of the CCN is now available at http://phenix-online.org/newsletter/ Articles include · Fitting tips #16 – Vicinal disulfides: Have you seen one of these strange gems? · CaBLAM: A C-Alpha Based Low-resolution Annotation Method for secondary structure and

[ccp4bb] Postdoc opening at Ailong Ke's lab, Cornell University

A NIH-funded postdoctoral position in structural biology is open in Prof. Ailong Ke’s laboratory at Cornell University, Ithaca, NY, USA. The research projects seek to understand the structure and function of RNA-protein complexes in CRISPR-Cas and

[ccp4bb] Issue with high Rfree (0.25) for a high-resolution dataset (1.05 Ang)

Hi all, I have a 1.05 Angstrom dataset that I was able to phase but the refined model only has an Rfree of approximately 0.25. The dataset includes 1800 images and, as the crystal did not suffer significantly from radiation damage, comprises all 360 deg. Auto-processing pipelines at diamond

[ccp4bb] Job Opening at Albert Einstein College of Medicine

A Postdoctoral Position in Structural Biology, Enzymology and Drug Development A position for a NIH-funded postdoctoral fellow is available immediately in the Syun-Ru Yeh Laboratory at Albert Einstein College of Medicine. The postdoctoral fellow will take a lead in (1) elucidating structure

[ccp4bb] AW: [EXTERNAL] [ccp4bb] Weird diffraction pattern

To me, it looks like some intergrown salt crystal. HS Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Sam Tang Gesendet: Dienstag, 9. Oktober 2018 13:13 An: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] [ccp4bb] Weird diffraction pattern Dear all Hello. We recently shot a

Re: [ccp4bb] Weird diffraction pattern

Hello again It could be a powder pattern aligned along one axis? The cell I gave (actually orthorhombic) is one of the crystal forms of one of the components in your mixture – glycerol. You may have another form of glycerol. It is worth checking. Colin PS I think glycerol diffraction has been

Re: [ccp4bb] Weird diffraction pattern

Hello Colin Although the unit cell dimensions from mosflm should be largely unreliable in this case, the software actually returned a P2 space group with a=24.6, b=7.5, c=69.5 where b is so short that it resembles a small molecule crystal. Regards Sam Sam On Tue, 9 Oct 2018 at 20:53,

Re: [ccp4bb] Weird diffraction pattern

Sam Would this unit cell index some of the spots? a = 7.00 ± 0.04 A, b = 9.96 ± 0.05 A, c = 6.29 ± 0.04 A. Colin From: CCP4 bulletin board On Behalf Of Sam Tang Sent: 09 October 2018 12:13 To: ccp4bb Subject: [ccp4bb] Weird diffraction pattern Dear all Hello. We recently shot a crystal (a

[ccp4bb] Job Opening at Diamond Light Source

Dear All We are recruiting a senior support scientist to join the MX group at Diamond Light Source. The role involves developing and supporting the very active MX groups user programme, user support for our international user community, training and providing operational support to the group.