1T92: Difference between revisions
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The pseudopilin PulG is one of several essential components of the type II pullulanase secretion machinery (the Pul secreton) of the Gram-negative bacterium ''Klebsiella oxytoca''. | The pseudopilin PulG is one of several essential components of the type II pullulanase secretion machinery (the Pul secreton) of the Gram-negative bacterium ''Klebsiella oxytoca''. | ||
The structure of PulG was solved from good 2-wavelength MAD data @ 2.8 Å. The raw data are available at | The structure of PulG was solved from good 2-wavelength MAD data @ 2.8 Å. The raw data are available at https://{{SERVERNAME}}/pub/datasets/ . | ||
Reference: Köhler, R., Schäfer, K., Müller, S., Vignon, G., Diederichs, K., Philippsen, A., Ringler, P., Pugsley, A.P., Engel, A., Welte, W. (2004) Structure and assembly of the pseudopilin PulG. ''Molecular Microbiology'' '''54''', 647-664. | Reference: Köhler, R., Schäfer, K., Müller, S., Vignon, G., Diederichs, K., Philippsen, A., Ringler, P., Pugsley, A.P., Engel, A., Welte, W. (2004) Structure and assembly of the pseudopilin PulG. ''Molecular Microbiology'' '''54''', 647-664. |
Latest revision as of 18:22, 24 March 2020
PulG
The pseudopilin PulG is one of several essential components of the type II pullulanase secretion machinery (the Pul secreton) of the Gram-negative bacterium Klebsiella oxytoca.
The structure of PulG was solved from good 2-wavelength MAD data @ 2.8 Å. The raw data are available at https://wiki.uni-konstanz.de/pub/datasets/ .
Reference: Köhler, R., Schäfer, K., Müller, S., Vignon, G., Diederichs, K., Philippsen, A., Ringler, P., Pugsley, A.P., Engel, A., Welte, W. (2004) Structure and assembly of the pseudopilin PulG. Molecular Microbiology 54, 647-664. doi:10.1111/j.1365-2958.2004.04307.x
XDS.INP for remote high (rh) data
JOB=XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT ! for this experiment: ORGX=1031 ORGY=1010 DETECTOR_DISTANCE=220 OSCILLATION_RANGE=1 X-RAY_WAVELENGTH=0.97857 NAME_TEMPLATE_OF_DATA_FRAMES=images/pulg_semet_D22_2_???.img DIRECT TIFF DATA_RANGE=5 124 SPOT_RANGE=5 124 BACKGROUND_RANGE=5 14 SPACE_GROUP_NUMBER=179 UNIT_CELL_CONSTANTS= 85.5 85.5 145.2 90 90 120 FRIEDEL'S_LAW=FALSE STRICT_ABSORPTION_CORRECTION=TRUE ! parameters with changes wrt default values: VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS=8000. 30000. TRUSTED_REGION=0. 0.99 MINIMUM_ZETA=0.05 INCLUDE_RESOLUTION_RANGE=50 0 STRONG_PIXEL=6 REFINE(INTEGRATE)=CELL BEAM ORIENTATION ! parameters specifically for this detector and beamline: NX=2048 NY=2048 QX=0.079092 QY=0.079092 ! MARCCD 165mm version DETECTOR=CCDCHESS MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD=65000 DIRECTION_OF_DETECTOR_X-AXIS=1 0 0 DIRECTION_OF_DETECTOR_Y-AXIS=0 1 0 INCIDENT_BEAM_DIRECTION=0 0 1 ROTATION_AXIS=1 0 0 FRACTION_OF_POLARIZATION=0.99 POLARIZATION_PLANE_NORMAL=0 1 0
XDS.INP for inflection point (ip) data
same as above, except
X-RAY_WAVELENGTH=0.97972 NAME_TEMPLATE_OF_DATA_FRAMES=images/pulg_semet_D22_3_???.img DIRECT TIFF DATA_RANGE=1 120 SPOT_RANGE=1 120 BACKGROUND_RANGE=1 10
XSCALE.INP
RESOLUTION_SHELLS= 10 6 5 4 3 2.9 2.8 SPACE_GROUP_NUMBER=179 UNIT_CELL_CONSTANTS= 85.71 85.71 145.34 90 90 120 OUTPUT_FILE=D22-rh.ahkl FRIEDEL'S_LAW=FALSE STRICT_ABSORPTION_CORRECTION=TRUE INPUT_FILE= ../xds_rh_2008/XDS_ASCII.HKL XDS_ASCII 50 2.8 OUTPUT_FILE=D22-ip.ahkl FRIEDEL'S_LAW=FALSE STRICT_ABSORPTION_CORRECTION=TRUE INPUT_FILE= ../xds_ip_2008/XDS_ASCII.HKL XDS_ASCII 50 2.8
running xdsconv for both rh and ip
cat > XDSCONV.INP<<eof INPUT_FILE=D22-rh.ahkl OUTPUT_FILE=D22-rh.hkl SHELX FRIEDEL'S_LAW=FALSE eof xdsconv cat > XDSCONV.INP<<eof INPUT_FILE=D22-ip.ahkl OUTPUT_FILE=D22-ip.hkl SHELX FRIEDEL'S_LAW=FALSE eof xdsconv
SHELXC and SHELXD
shelxc pulg<<eof INFL D22-ip.hkl HREM D22-rh.hkl CELL 85.71 85.71 145.34 90 90 120 SPAG P6522 MAXM 2 eof cat > pulg_fa.ins <<eof TITL pulg_fa.ins MAD in P6522 CELL 0.98000 85.71 85.71 145.34 90.00 90.00 120.00 LATT -1 SYMM -Y, X-Y, 2/3+Z SYMM -X+Y, -X, 1/3+Z SYMM -X, -Y, 1/2+Z SYMM Y, -X+Y, 1/6+Z SYMM X-Y, X, 5/6+Z SYMM Y, X, 2/3-Z SYMM X-Y, -Y, -Z SYMM -X, -X+Y, 1/3-Z SYMM -Y, -X, 1/6-Z SYMM -X+Y, Y, 1/2-Z SYMM X, X-Y, 5/6-Z SFAC SE UNIT 384 SHEL 999 3.3 PATS FIND 8 MIND -1.5 -0.1 NTRY 100 SEED 1 HKLF 3 END eof shelxd pulg_fa