A direct-method aided fragment extension procedure without using SAD/SIR information has been
successfully tested. This enables the combination of direct methods with the molecular replacement method.
The direct-method probability formula for breaking the SAD/SIR phase ambiguity has been redefined such that
in the expression , j' is the phase
contributed from the randomly selected 5% of the starting model, while |Δj|
is the absolute phase difference between the starting model and j'.
Then the formula
is used to calculate the sign preceding |Δj|. The procedure
has been tested with the diffraction data of acidic phospholipase A2 from agkistrodon halys pallas at 2.0Å
resolution. Starting from a model containing 48 of the total of 124 residues, two cycles of the iteration
OASIS+DM+ARP/wARP led to a model containing 123 residues all docked into the sequence.
For a comparison, the same starting model was input to the iteration of DM+ARP/wARP without using OASIS.
The initial model completely corrupted at the third cycle indicating the failure of iteration.
By Y. He1, D.Q. Yao1, 2, 3, Y.X. Gu1, C.D. Zheng1, H.F. Fan1 & Z.J. Lin4,
1Institue of Physics, Chinese Academy of Sciences, Beijing 100080, China
2Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
3National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei
230026, China
4Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China