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1RQW: Difference between revisions
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== SAD: Peak data alone == | == SAD: Peak data alone == | ||
=== manual structure solution using hkl2map and buccaneer === | === manual structure solution using hkl2map and buccaneer === | ||
The structure was solved using the [http://schneider.group.ifom-ieo-campus.it/hkl2map/ hkl2map] GUI. Based on | The structure was "solved" using the [http://schneider.group.ifom-ieo-campus.it/hkl2map/ hkl2map] GUI. Based on | ||
[[Image:1rqw-peak-self-anomCC-resolution.png]] [[Image:1rqw-peak-d"sig-resolution.png]] | [[Image:1rqw-peak-self-anomCC-resolution.png]] [[Image:1rqw-peak-d"sig-resolution.png]] | ||
I decided to use 3.3 Å as a suitable cutoff for solving the substructure. SHELXD then found | I decided to use 3.3 Å as a suitable cutoff for solving the substructure, and to let SHELXD search for 20 Br atoms (just a guess!). SHELXD then found a convincing solution: | ||
[[Image:1rqw-peak-ccall-ccweak.png]] [[Image:1rqw-peak-histogram-ccall.png]] [[Image:1rqw-peak-occupancy.png]] | [[Image:1rqw-peak-ccall-ccweak.png]] [[Image:1rqw-peak-histogram-ccall.png]] [[Image:1rqw-peak-occupancy.png]] | ||
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[[Image:1rqw-peak-contrast.png]] [[Image:1rqw-peak-connectivity.png]] [[Image:1rqw-peak-estimated-ccmap.png]] | [[Image:1rqw-peak-contrast.png]] [[Image:1rqw-peak-connectivity.png]] [[Image:1rqw-peak-estimated-ccmap.png]] | ||
=== automatic structure solution using Auto-Rickshaw === | Using ccp4i, I imported the .phs file from SHELXE, gave it to ccp4i's buccaneer- autobuild/refine task using default parameters, and obtained in the third cycle from buccaneer 0.9.9: | ||
202 residues were built in 9 chains, the longest having 57 residues. | |||
138 residues were sequenced, after pruning. | |||
Refmac5 refined this to R/R_free of 39.0%/42.4% which shows that the structure is essentially solved. | |||
=== automatic structure solution using Auto-Rickshaw (http://www.embl-hamburg.de/Auto-Rickshaw/) === | |||
This uses Santosh Panjikar's script DPS2AR.csh: | This uses Santosh Panjikar's script DPS2AR.csh: | ||
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email kay.diederichs@uni-konstanz.de sequencefile 1rqw.seq | email kay.diederichs@uni-konstanz.de sequencefile 1rqw.seq | ||
thau-peak-I.mtz was obtained in two steps: | |||
a) generating temp.hkl from XDS_ASCII.HKL with the following XDSCONV.INP: | |||
INPUT_FILE=XDS_ASCII.HKL | |||
OUTPUT_FILE=temp.hkl CCP4_I ! Warning: do _not_ name this file "temp.mtz" ! | |||
FRIEDEL'S_LAW=FALSE ! default is FRIEDEL'S_LAW=TRUE | |||
b) running the conversion to thau-peak-I.mtz as indicated by the XDSCONV screen output. | |||
1rqw.seq is | |||
ATFEIVNRCS YTVWAAASKG DAALDAGGRQ LNSGESWTIN VEPGTKGGKI WARTDCYFDD | ATFEIVNRCS YTVWAAASKG DAALDAGGRQ LNSGESWTIN VEPGTKGGKI WARTDCYFDD | ||
SGSGICKTGD CGGLLRCKRF GRPPTTLAEF SLNQYGKDYI DISNIKGFNV PMDFSPTTRG | SGSGICKTGD CGGLLRCKRF GRPPTTLAEF SLNQYGKDYI DISNIKGFNV PMDFSPTTRG | ||
CRGVRCAADI VGQCPAKLKA PGGGCNDACT VFQTSEYCCT TGKCGPTEYS RFFKRLCPDA | CRGVRCAADI VGQCPAKLKA PGGGCNDACT VFQTSEYCCT TGKCGPTEYS RFFKRLCPDA | ||
FSYVLDKPTT VTCPGSSNYR VTFCPTA | FSYVLDKPTT VTCPGSSNYR VTFCPTA | ||
The result of this is a model that only lacks residues 1, 82, 83, 207, and which has a "core RMS" (from coot's SSM superpose) of 0.14 Å against 1rqw (which is a 1.05 Å structure). | |||
It couldn't be simpler than that. Thanks, Santosh! | |||