1T92

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