We are using the SP parallel supercomputer to determine the X-ray crystal structure of acetyl xylan esterase (AXE) using a new ab initio phasing procedure. The procedure is based on the joint probability distribution between measured X-ray intensities and their unknown phases. The overall problem is expressed in terms of the global, constrained minimum for a function in which the unknown phases are variables. The procedure has been implemented as a computer program called Shake-and-Bake (SnB) which has recently been tested on the IBM SP2 at Cornell. Although direct phasing methods have been routinely used to solve structures with 100 or fewer atoms, protein structures are usually determine by other methods. Recently, however, the structure of androctonus scorpion toxin II, which contains 620 non-hydrogen atoms was routinely solved using the SnB program. AXE is an enzyme containing 1500 non-hydrogen atoms and its structure is currently unknown. X-ray intensity data for AXE were measured to 0.9 resolution at the Cornell High Energy Synchrotron Source (CHESS). Successful application of SnB in the structure determination of AXE will represent an important advance in the field of macromolecular crystallography. Proof that large protein structures can be determined from intensity data alone, without the use of heavy-atom derivatives, will pave the way for further development and optimization of the computer algorithms. When this happens, many new protein structures may be determined using these methods which will require days rather than months (or years) to produce results.
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