Content
See also the PDB summary and the paper.
From a simlpe autoPROC run we have 3 datasets (hrem, peak and infl) for a Se-MET MAD experiment.
We also have the sequence of a HasR and HasA heterodimer (13 Met in HasR and 3 in HasA):
AQAEASSAQAAQQKNFNIAAQPLQSAMLRFAEQAGMQVFFDEVKLDGMQAAALNGSMSVEQGLRRLIGGNPVAFRLQPQG QIVLSRLPTANGDGGALALDSLTVLGAGGNNANDWVYDEPRSVSVISREQMDNRPARHAADILEQTTGAYSSVSQQDPAL SVNIRGIQDYGRVNMNIDGMRQNFQKSGHGQRNGTMYIDSELLSGVTIDKGTTGGMGSAGTLGGIATFNTVSASDFLAPG KELGGKLHASTGDNGTHFIGSGILALGNETGDILLAASERHLGDYWPGNKGDIGNIRINNDTGNYDRYAESIKNNKIPDT HYRMHSRLAKVGWNLPANQRLQLSYLQTQTASPIAGTLTNLGTRPPYELGWKRTGYTDVMARNAAFDYSLAPEDVDWLDF QAKLYYVDTQDDSDTYSTSSLLDNGYATRTRLRTYGAQAQNTSRFSLAPGHDFRANYGLEFYYDKATSDSSRQGMEGVTP AGNRSVASLFANLTYDYDGWLTLEGGLRYDRYRLRGQTGLSYPDLAKDGQRYTIDNPCKALRLTGCSTTTREDWDVDRDQ GKLSPTLAVAVRPGVEWLELYTTYGKSWRPPAITETLTNGSAHSSSTQYPNPFLQPERSRAWEVGFNVQQPDLWFEGDRL VAKVAYFDTKVDNYINLAIDRNKPGLVQPSIGNAAYVNNLSKTRFRGLEYQLNYDAGVFYADLTYTHMIGKNEFCSNKAW LGGRLRYGDGSRRGNFYVEPDAASNDFVTCDGGTQFGSAAYLPGDRGSVTLGGRAFDRKLDAGVTVRFAPGYQDSSVPSN YPYLADWPKYTLFDLYASYKLTDSLTLRGSVENLTNRAYVVSYGETLANTLGRGRTVQGGVEYRF MRGSHHHHHHGIRMRARYPAFSVNYDSSFGGYSIHDYLGQWASTFGDVNHTNGNVTDANSGGFYGGSLSGSQYAISSTAN QVTAFVAGGNLTYTLFNEPAHTLYGQLDSLSFGDGLSGGDTSPYSIQVPDVSFGGLNLSSLQAQGHDGVVHQVVYGLMSG DTGALETALNGILDDYGLSVNSTFDQVAAATAVGVQHADSPELLAA
We start autoSHARP through the default (httpd-based) interface and give it the following information for a 3-wavelength MAD experiment:
which after 90 minutes gives us a density map to look at:
This has very nice secondary structure and seems to show two complete molecules.
Files:
Feeding those (solvent-flattened) phases into a new tool we're developing (combining density modification using PARROT and model building using BUCCANEER, both programs by K. Cowtan):
% ljs -mtz eden_flat_64.8pc.mtz -fast -seq ../../datafiles/3CSL.pir
gives after 30 minutes a model of 1838 residues with 902 (out of 2142 according the HasR and HasA sequence) docked. As a comparison, the PDB entry contains 1832 residues.
![]() |
![]() |
Running a little bit longer (just under an hour in total) gives 1869 residues with 1279 docked into the sequence:
![]() |
![]() |