2QVO.xds

XDS data reduction

This is a pared-down XDS.INP (obtained by egrep -v '^ *!' XDS.INP) based upon XDS-MARCDD.INP from the XDS distribution site - it has only those lines that are not commented out. To arrive here, one takes the steps outlined in Tutorial(First_Steps):

DETECTOR=CCDCHESS        MINIMUM_VALID_PIXEL_VALUE=1     OVERLOAD=65000
DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0
DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0
TRUSTED_REGION=0.0 0.99 !Relative radii limiting trusted detector region
MAXIMUM_NUMBER_OF_PROCESSORS=8!<25;ignored by single cpu version of xds
JOB=  XYCORR INIT COLSPOT IDXREF DEFPIX  INTEGRATE CORRECT
ORGX=2000 ORGY=2048  !Detector origin (pixels)! numbers are rough estimates w/ adxv
DETECTOR_DISTANCE= 125.0   !(mm)
ROTATION_AXIS= 1.0 0.0 0.0
OSCILLATION_RANGE=1.0            !degrees (>0)
X-RAY_WAVELENGTH=1.9         !Angstroem
INCIDENT_BEAM_DIRECTION=0.0 0.0 1.0
FRACTION_OF_POLARIZATION=0.95 !default=0.5 for unpolarized beam
POLARIZATION_PLANE_NORMAL= 0.0 1.0 0.0
SPACE_GROUP_NUMBER=0   !0 for unknown crystals; cell constants are ignored.
UNIT_CELL_CONSTANTS= 53 53 41   90 90 90
FRIEDEL'S_LAW=FALSE !Default is TRUE.
NAME_TEMPLATE_OF_DATA_FRAMES=../../g/040707-8_2_2_1.????  ! TIFF
DATA_RANGE=1 360       !Numbers of first and last data image collected
BACKGROUND_RANGE=1 5  !Numbers of first and last data image for background
SPOT_RANGE=1 180       !First and last data image number for finding spots
REFINE(IDXREF)=BEAM AXIS ORIENTATION CELL DISTANCE
REFINE(INTEGRATE)=DISTANCE BEAM ORIENTATION CELL !AXIS
REFINE(CORRECT)=DISTANCE BEAM ORIENTATION CELL AXIS
VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= 6000 30000 !Used by DEFPIX for excluding shaded parts of the detector.
INCLUDE_RESOLUTION_RANGE=50.0 0 !Angstroem; used by DEFPIX,INTEGRATE,CORRECT
MINIMUM_ZETA=0.1 !Defines width of 'blind region' (XPLAN,INTEGRATE,CORRECT)
WFAC1=1.5  !This controls the number of rejected MISFITS in CORRECT; a larger value leads to fewer rejections.
STRONG_PIXEL=6.0                              !used by: COLSPOT

The resulting output files are XYCORR.LP, INIT.LP, COLSPOT.LP, IDXREF.LP, DEFPIX.LP, INTEGRATE.LP and CORRECT.LP. Data files are XPARM.XDS (from IDXREF), and the XDS_ASCII.HKL file all of which can be downloaded from here.

SHELXC/D/E structure solution

generate XDSCONV.INP (a trick is to use MERGE=TRUE, for some reason the results are better that way) and run xdsconv and shelxc:

 #!/bin/csh -f

cat > XDSCONV.INP <<end
INPUT_FILE=../XDS_ASCII.HKL
OUTPUT_FILE=temp.hkl SHELX
MERGE=TRUE
FRIEDEL'S_LAW=FALSE
end

xdsconv 

shelxc j <<end
SAD   temp.hkl
CELL 53.10 53.10 40.90 90 90 90
SPAG P42
MAXM 2
end

This writes j_fa.ins, j.hkl, j_fa.hkl . However, we overwrite j.ins now:

cat > j_fa.ins <<end
TITL j_fa.ins SAD in P42
CELL  0.98000   53.10   53.10   40.90   90.00   90.00   90.00
LATT  -1
SYMM -Y, X, 1/2+Z
SYMM -X, -Y, Z
SYMM Y, -X, 1/2+Z
SFAC S
UNIT   128
SHEL 999 3.0
FIND 3
NTRY 100
MIND -1.0 2.2
ESEL 1.3
TEST 0 99
SEED 1
PATS
HKLF 3
END
end

shelxd j_fa

This gives best CC All/Weak of 35.61 / 26.03 . Next we run G. Sheldrick's beta-Version of shelxe Version 2009/4:

shelxe.beta -a6 -q j j_fa -h -s0.55 -m20 -b 

Some important lines in the output:

   79 residues left after pruning, divided into chains as follows:
A:  20   B:  22   C:  37

CC for partial structure against native data =  50.42 %
 <wt> = 0.300, Contrast = 0.731, Connect. = 0.817 for dens.mod. cycle 20
 Estimated mean FOM = 0.659   Pseudo-free CC = 68.71 %

clearly indicating that the structure is solved.

For completeness, we run the inverse hand:

shelxe.beta -a6 -q j j_fa -h -s0.55 -m20 -b -i

but of course this gives much worse statistics.