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Simulated-1g1c: Difference between revisions
→Solving the structure
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One hint towards the contents of the "crystal" is that the information about the simulated data contained the strings "1g1c". This structure | One hint towards the contents of the "crystal" is that the information about the simulated data contained the strings "1g1c". This structure (spacegroup 19, cell axes 38.3, 78.6, 79.6) is available from the PDB; it contains 2 chains of 99 residues, and a chain has 2 Cys and 2 Met. Thus we assume that the simulated data may represent SeMet-SAD. Using [[ccp4:hkl2map|hkl2map]], we can easily find four sites with good CCall/CCweak: | ||
[[File:Simulated-1g1c-ccall-ccweak2.png]] | [[File:Simulated-1g1c-ccall-ccweak2.png]] | ||
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shelxe.beta -m40 -a -q -h -s0.54 -b -i -e -n 1g1c 1g1c_fa | shelxe.beta -m40 -a -q -h -s0.54 -b -i -e -n 1g1c 1g1c_fa | ||
but it traces only about 62 residues. The density looks reasonable, though. | but it traces only about 62 residues. The density looks somewhat reasonable, though. | ||
The files [ftp: | The files [ftp://turn5.biologie.uni-konstanz.de/pub/xds-datared/1g1c/xds-simulated-1g1c-I.mtz xds-simulated-1g1c-I.mtz] and [ftp://turn5.biologie.uni-konstanz.de/pub/xds-datared/1g1c/xds-simulated-1g1c-F.mtz xds-simulated-1g1c-F.mtz] are available. | ||
I refined against 1g1c.pdb: | |||
phenix.refine xds-simulated-1g1c-F.mtz 1g1c.pdb refinement.input.xray_data.r_free_flags.generate=True | |||
The result was | |||
Start R-work = 0.3453, R-free = 0.3501 | |||
Final R-work = 0.2170, R-free = 0.2596 | |||
which appears reasonable. | |||