Comparison of phasing methods for sulfur-SAD using in-house chromium radiation: case studies for standard proteins and a 69 kDa protein.
Phasing of the crystal structures of four standard proteins (lysozyme, trypsin, glucose isomerase and thaumatin) and a novel 69 kDa protein from Thermus thermophilus, TT0570, was performed using the single-wavelength anomalous diffraction of S atoms intrinsically present within the native protein molecules. To utilize the sulfur anomalous diffraction, the data sets were collected using the loopless data-collection method with chromium Kalpha X-rays of wavelength 2.29 A. Three phasing methods, MLPHARE, SHARP and OASIS-2004, were tested in combination with the DM or SOLOMON density-modification method. The results showed that the solvent contents are still an important factor for phasing with the S-SAD method, even when longer wavelength Cr Kalpha radiation is used. Of the three procedures, the improved direct phasing of OASIS-2004 with its implemented fragment feedback to the direct-method probability calculation gave the best results in determining the initial phases. For all five proteins, almost the entire models could be built automatically.
Watanabe
Nobuhisa
N
Graduate School of Science, Hokkaido University, Sapporo 0600810, Japan. nobuhisa@sci.hokudai.ac.jp
Kitago
Yu
Y
Tanaka
Isao
I
Wang
Jia wei
Jw
Gu
Yuan xin
Yx
Zheng
Chao de
Cd
Fan
Hai fu
Hf
D019747:Aldose-Ketose Isomerases / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry; D018360:Crystallography, X-Ray / Q000379:methods*; D008958:Models, Molecular; D009113:Muramidase / Q000737:chemistry; D010940:Plant Proteins / Q000737:chemistry; D011506:Proteins / Q000737:chemistry*; D013455:Sulfur / Q000737:chemistry; D014357:Trypsin / Q000737:chemistry
D001426:Bacterial Proteins; D010940:Plant Proteins; D011506:Proteins; C003427:thaumatin protein, plant; D013455:Sulfur; D009113:Muramidase; D014357:Trypsin; D019747:Aldose-Ketose Isomerases; C023298:xylose isomerase