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Simulated-1g1c: Difference between revisions
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but it traces only about 62 residues. The density looks somewhat reasonable, though. | but it traces only about 62 residues. The density looks somewhat reasonable, though. | ||
The files [ftp:// | The files [ftp://{{SERVERNAME}}/pub/xds-datared/1g1c/xds-simulated-1g1c-I.mtz xds-simulated-1g1c-I.mtz] and [ftp://{{SERVERNAME}}/pub/xds-datared/1g1c/xds-simulated-1g1c-F.mtz xds-simulated-1g1c-F.mtz] are available. | ||
I refined against 1g1c.pdb: | I refined against 1g1c.pdb: | ||
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showing that the anomalous completeness, and even the quality of the anomalous signal, can indeed be increased. I doubt, however, that going to three or more frames would improve things even more. | showing that the anomalous completeness, and even the quality of the anomalous signal, can indeed be increased. I doubt, however, that going to three or more frames would improve things even more. | ||
The MTZ files are at [ftp:// | The MTZ files are at [ftp://{{SERVERNAME}}/pub/xds-datared/1g1c/xds-simulated-1g1c-F-2frames.mtz] and [ftp://{{SERVERNAME}}/pub/xds-datared/1g1c/xds-simulated-1g1c-I-2frames.mtz], respectively. They were of course obtained with XDSCONV.INP: | ||
INPUT_FILE=temp.ahkl | INPUT_FILE=temp.ahkl | ||
OUTPUT_FILE=temp.hkl CCP4_I | OUTPUT_FILE=temp.hkl CCP4_I | ||
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</pre> | </pre> | ||
Using the default (see above) phenix.refine job, I obtain against the [ftp:// | Using the default (see above) phenix.refine job, I obtain against the [ftp://{{SERVERNAME}}/pub/xds-datared/1g1c/xds-simulated-1g1c-F-2frames.mtz MTZ file with amplitudes]: | ||
Start R-work = 0.3434, R-free = 0.3540 | Start R-work = 0.3434, R-free = 0.3540 | ||
Final R-work = 0.2209, R-free = 0.2479 | Final R-work = 0.2209, R-free = 0.2479 | ||
and against the [ftp:// | and against the [ftp://{{SERVERNAME}}/pub/xds-datared/1g1c/xds-simulated-1g1c-I-2frames.mtz MTZ file with intensities] | ||
Start R-work = 0.3492, R-free = 0.3606 | Start R-work = 0.3492, R-free = 0.3606 | ||
Final R-work = 0.2244, R-free = 0.2504 | Final R-work = 0.2244, R-free = 0.2504 | ||
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total 165799 42025 43003 97.7% 11.7% 12.3% 162399 10.07 13.5% 14.8% 17% 0.908 16219 | total 165799 42025 43003 97.7% 11.7% 12.3% 162399 10.07 13.5% 14.8% 17% 0.908 16219 | ||
Using these data (stored in [ftp:// | Using these data (stored in [ftp://{{SERVERNAME}}/pub/xds-datared/1g1c/xscale.oldversion]), I was finally able to solve the structure (see screenshot below) - SHELXE traced 160 out of 198 residues. All files produced by SHELXE are in [ftp://{{SERVERNAME}}/pub/xds-datared/1g1c/shelx]. | ||
[[File:1g1c-shelxe.png]] | [[File:1g1c-shelxe.png]] | ||