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! | |||
Revision as of 17:40, 1 May 2008
Thaumatin Br soak: structure solution from either 2-wavelength MAD, or from single wavelength SAD
Prior to flash cooling in liquid nitrogen at 100 K the crystals were soaked for a few seconds in a solution containing 1 M sodium bromide and 25% (v/v) glycerol.
The peak and inflection datasets (360 images each) are available from the EMBL Hamburg website. The XDS data reductions are here.
Data reduction was performed starting with the template for the MarCCD 225 detector, changing
ORGX=1533 ORGY=1536 DETECTOR_DISTANCE=200 OSCILLATION_RANGE=0.5 X-RAY_WAVELENGTH=0.91878 ! peak ! X-RAY_WAVELENGTH=0.9196 ! inflection NAME_TEMPLATE_OF_DATA_FRAMES=../peak/thau_peak_1_???.mccd DIRECT TIFF ! NAME_TEMPLATE_OF_DATA_FRAMES=../inf/thau_inf_1_???.mccd DIRECT TIFF DATA_RANGE=1 360 SPACE_GROUP_NUMBER=92 UNIT_CELL_CONSTANTS= 57.8 57.8 150. 90 90 90 FRIEDEL'S_LAW=FALSE VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS=9000. 30000.
SAD: Peak data alone
manual structure solution using hkl2map and buccaneer
The structure was "solved" using the hkl2map GUI. Based on
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:
and SHELXE produced useful phases:
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:
DPS2AR.csh datafile1 thau-peak-I.mtz keeps world ver completeversion nres 207 nsm 20 masu 1 meth SAD SG P41212 \
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 SGSGICKTGD CGGLLRCKRF GRPPTTLAEF SLNQYGKDYI DISNIKGFNV PMDFSPTTRG CRGVRCAADI VGQCPAKLKA PGGGCNDACT VFQTSEYCCT TGKCGPTEYS RFFKRLCPDA 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!