CCP4 Grant Renewal 2014-2019: Question-driven crystallographic data collection and advanced structure solution

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This proposal incorporates five related work packages.

In WP1 we will track synchrotron-collected data through computational structure determination, to find whether the most useful data can be recognised a priori using established or novel metrics of data quality and consistency. We will then enable data collection software to communicate with pipelines and graphics programs to assess when sufficient data have been collected for a given scientific question, and so to prioritise further beamtime usage. We will also communicate extra information about diffraction data to structure determination programs, and so support the statistical models and algorithms being developed in WP4.

WP2 will improve the key MR step of model preparation, especially from diverged, NMR, or ab initio models. One development will be to extend the size limit of ab initio search model generation by exploiting sequence covariance algorithms.

In WP3 we will use our description of electron density maps as a field of control points to better use electron density or atomic models positioned by MR. Restrained manipulation of these points provides a low-order parameterisation of refinement decoupled from atomic models, and therefore suitable for highly diverged atomic models or EM-derived maps. We will extend this approach to characterise local protein mobility without the requirement of TLS for predefinition of rigid groups.

In WP4 we will statistically model non-idealities in experimental data, including non isomorphism, spot overlap, and radiation damage. The resulting models, implemented in REFMAC, will be applied to refinement using data that are annotated by WP1 tools and tracked by WP0.

WP0 will provide the tools to integrate the other WPs. For this, it will create a cloud environment where storage- and compute-resources can be utilised optimally, and where rich information can be passed among beamlines, pipelines, and graphics programs.

With the tremendous improvements in beamline technology it is in principle possible to collect many high quality datasets per hour on a single synchrotron beamline. Nevertheless few of these datasets convert to useful structures. Recognizing the potential impact on the academic and commercial structural biology of improving this success rate Diamond Light Source is directing effort and resource towards increasing productively for the most challenging problems while also making low hanging fruit routine work. For straightforward cases automated pipelines can perform the bulk of the data analysis, in successful cases leading quickly to a partially or fully built molecular model. However, in the most difficult cases the benefits of automation are to mainly take over the most laborious, time-consuming tasks (e.g. sample exchange, automated assessment of diffraction strength and sample alignment), enabling the crystallographer to focus effort on the more complex tasks. Automated data analysis frequently fails in such challenging cases, typically because they require multiple sets of data from multiple crystal samples to be gathered together in a unique way. The current set of Diamond automated pipelines are linear brute-force systems using high performance computing to attempt structure solution on virtually every data set recorded from the beamlines, however users get little feedback to help improve their measurements or analysis. The provision of robust metrics within data analysis streams and their implementation in decision making algorithms will transform the way structural biologist perform synchrotron experiments by

1) rationalising the use of beam time and increasing data set to structure conversion rate
2) providing users with a visual way of assessing data quality at every stage of analysis
3) facilitating decisions about ongoing experiments based on prior data and ongoing analysis
4) making more efficient use of HPC resource by prioritizing jobs based on likelihood of success
5) drastically reducing the distance between diffraction experiments and useful electron density

This package of work will be running in parallel with the DIALS project (a collaboration between Diamond, CCP4 and other European partner synchrotrons) that will deliver advanced data integration software to tackle weaker and high mosaicity data while addressing the very rapid frame rates (>100 Hz) expected from next generation detectors. Together, the delivery of the DIALS software to synchrotrons by 2015 and the provision of assisted data collection and analysis tools from WP1 connected to CCP4 Cloud infrastructure from WP0 will create the opportunity for a leap forward in the level complexity of crystallographic problem that UK users can address.

Diamond and CCP4 both have a track record in training students and young researchers. The tools developed within this grant will be promoted through practical workshops and courses specifically aimed at increasing the level of crystallographic expertise of our next generation of UK structural biologists.

As part of Diamond's continued engagement with the general public several open days are run yearly to communicate the science and technology of Diamond in an entertaining and memorable fashion. The use of visual props and games to explain the fundamental ideas and the importance of crystallography in biology and medicine has been a major part of this. Diamond/CCP4 cooperation in this project will provide an ideal opportunity to showcase CCP4's and the UK's contribution to biological crystallography over decades.