Computational protocol: DNA binding mechanism revealed by high resolution crystal structure of Arabidopsis thaliana WRKY1 protein

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Protocol publication

[…] Two crystal forms were obtained from the same growth condition. One belongs to the space group P21, with diffraction to 2.5 Å resolution at home X-ray sources as published before (), whereas the other crystal form belongs to the space group P3221, and diffracted to better than 1.6 Å at beamline 3W1A of Beijing Synchrotron Radiation Facilities (BSRF). Diffraction data were collected on a MAR165 CCD camera (MARresearch GmbH, Hamburg). The wavelength was set to 1.24 Å, at the higher energy side of the absorption peak of zinc. The data with anomalous signals were processed using the program DENZO and SCALEPACK (). The statistics for the X-ray data collection and processing of the P3221 crystal form are summarized in . The zinc site was located using the program SHELXD () and the heavy atom parameters were refined using the program SOLVE (). The initial phases were obtained by the program OASIS-2004 (), then refined by using the program DM (CCP4) (). Finally, ARP/warp () was used for the model auto-building.Since the initial phases and auto-traced model were of good qualities, the subsequent refinement work could be easily carried out by using the program CNS (). Manual adjustment of the structure was done with the program O (), and a succinic acid as well as water molecules were added into the positive difference densities. The final model was refined by REFMAC5 (). […]

Pipeline specifications

Software tools SHELX, CCP4, ARP/wARP, CNS, REFMAC5
Application Protein structure analysis
Organisms Arabidopsis thaliana
Chemicals Zinc, Salicylic Acid