Here, we test the new methods described above on a wide range of real SAD, MAD and SIRAS merged diffraction data sets. For our tests, only the intensities or structure-factor amplitudes, along with the sequence for a protein monomer, the number of substructure atoms expected per monomer and the f′ and f′′ values for the substructure atoms were input. CRANK used AFRO and CRUNCH2 for substructure detection, BP3 for substructure phasing and SOLOMON with MULTICOMB for density modification. Three cycles of Buccaneer iterated with REFMAC were used for automated model building with iterative refinement. The default options or parameters were used in all programs. The defaults set by CRANK depend upon the particular experiment: for SAD data, AFRO uses the multivariate |FA| value calculation and MULTICOMB uses the multivariate SAD function for phase combination in density modification, while Buccaneer uses the SAD function implemented in REFMAC. For SIRAS data, AFRO calculates |FA| from either the anomalous signal or using isomorphous differences by determining which signal is greater. BP3 uses the uncorrelated SIRAS function described previously (Pannu et al., 2003 ▶ ) and SOLOMON uses MLHL phase combination in MULTICOMB, while Buccaneer uses the multivariate SIRAS function in REFMAC. Finally, for MAD data AFRO chooses the wavelength with the greatest anomalous signal and calculates multivariate FA values from it. Similar to SIRAS data, SOLOMON uses MLHL phase combination in MULTICOMB to perform density modification and Buccaneer uses the MLHL likelihood function in REFMAC for model refinement.
In the test cases below, the previous version of CRANK, version 1.3, is tested with the current version, version 1.4. The main differences between the two versions are the development version of AFRO that calculates multivariate |FA| values given SAD data and the use of MULTICOMB for phase combination in density modification, which were both introduced in version 1.4.
In total, we report results from 116 real data sets from several different sources listed in Appendix A . The data sets cover a wide range of resolutions (from 0.94 to 3.29 Å) and anomalous scatterers, including selenium, sulfur, chloride, sulfate, manganese, bromide, calcium and zinc. Of the 116 data sets, 63 are MAD data sets, 46 are SAD data sets and seven are SIRAS data sets.
In the test cases below, the previous version of CRANK, version 1.3, is tested with the current version, version 1.4. The main differences between the two versions are the development version of AFRO that calculates multivariate |FA| values given SAD data and the use of MULTICOMB for phase combination in density modification, which were both introduced in version 1.4.
In total, we report results from 116 real data sets from several different sources listed in Appendix A
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