Quality Control

This article is under construction! This is an attempt of putting together a number of datasets with different characteristics (high and low resolution, good and bad crystals, untwinned and twinned), their evaluation with different versions of XDS, and the determination of the quality of the resulting data using refinement and phasing.

The goal of this project is to find generally optimal parameters for XDS data reduction, to monitor the progress of the program, and to discover bugs or regressions.

I'm currently working with Qingping Xu on identifying suitable datasets in the (publicly accessible!) JCSG dataset archive.

PulG (good 2-wavelength MAD data @ 2.8 A)

Raw data: ftp://turn5.biologie.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. [1]

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