Crystal Structure Determination of Pfu-1210814 in 4.5 Hours

The crystal structure determination of structural genomics protein Pfu-1210814 was the first application of the SCA2STRUCTURE pipeline in a real case. The anomalous diffraction data was collected at SER-CAT beamline using 0.97Å wavelength X-ray during the SER-CAT training in July 11-12, 2002. The data was immediately put into the SCA2STRUCTURE pipeline and 85% of the model was correctly traced. The total time used from mounted crystal to traced model is 4.5 hours. Domain swapping is found in this structure.

High-throughput Crystal Structure Determination Pipelines (StructureWise)

Two crystallographic structure determination pipelines (MRPIPE and SCA2STRUCTURE) have been implemented on a 128-processor Linux cluster to meet the need of high throughput crystal structure determination. MRPIPE is a molecular replacement pipeline using EPMR and AMORE. With input of initial scaled structure factors, MRPIPE will spawn jobs in parallel on the cluster searching models of Psi-BLAST filtered homologous structures, non-redundant PDB structures or predicted structures. The resulting phases are passed to Arp/wARP for automated fitting and refinement. SCA2STRUCTURE was developed to pipeline the process of solving new crystal structures from scaled diffraction data. The current version chains SOLVE/RESOLVE, ISAS, DM, SOLOMON and Arp/wARP into a pipeline that spawns hundreds of jobs using various combinations of program input parameters. In this way SCA2STRUCTURE screens a broad range of parameter space for heavy atom searching/refinement, phasing, tracing and refinement. .

New NMR Approach to Backbone Structure Determination

The NMR core at the SECSG has taken its first step toward implementing a new NMR based approach to the determination of protein backbone structures (Tian et al. J. Am. Chem. Soc. 123: 11791-11796, 2001). The approach is based on collection of residual dipolar coupling data that yield orientation constraints on bonds along the polypeptide backbone, and on analysis using a procedure that doesn't require prior assignment of resonances. Acquisition of data required about 10% of the time needed for traditional NOE based approaches to protein structure determination. The first application to a small protein, rubredoxin, produced a structure that agreed with an X-ray structure of a nearly identical protein to within 1.8Å rmsd. An illustration of the superimposed structures is given in the picture.