2GIF

Structural asymmetry of AcrB trimer suggests a peristaltic pump mechanism

The structure of AcrB in spacegroup C2 was solved by molecular replacement (using the symmetric structure as a model), followed by many cycles of refinement and model building. The raw data are available at ftp://turn5.biologie.uni-konstanz.de/pub/datasets/ .

Reference: Seeger, M.A., Schiefner, A., Eicher, T., Verrey, F., Diederichs, K., Pos, K.M. (2006) Structural Asymmetry of AcrB Trimer Suggests a Peristaltic Pump Mechanism. Science 313: 1295-1298

The goal of this XDSwiki project is to run different versions of XDS (and other data reduction programs if anybody would contribute the data reductions!), and to compare internal R-factor statistics against R-factors of the refined model.

A suitable XDS.INP should be:

JOB= XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT
MINIMUM_ZETA=0.05
ORGX=1546    ORGY=1526
DETECTOR_DISTANCE= 300
OSCILLATION_RANGE=1.0            !degrees (>0)
X-RAY_WAVELENGTH=1.0       !Angstroem
MAXIMUM_NUMBER_OF_PROCESSORS=16
NAME_TEMPLATE_OF_DATA_FRAMES=frms/ms424_2_???.img DIRECT  TIFF
DATA_RANGE=1  200  
SPOT_RANGE=1  200   
BACKGROUND_RANGE=1 10 
SPACE_GROUP_NUMBER=5   !0 for unknown crystals; cell constants are ignored.
UNIT_CELL_CONSTANTS= 223.3  134.3  161.2  90.0  98.2  90.0
REFINE(IDXREF)=BEAM AXIS ORIENTATION CELL DISTANCE
REFINE(INTEGRATE)=DISTANCE BEAM ORIENTATION CELL !AXIS
REFINE(CORRECT)=DISTANCE BEAM ORIENTATION CELL AXIS
NX=3072 NY=3072 QX=0.0732  QY=0.0732   !MARCCD 225mm version
ROTATION_AXIS= 1.0 0.0 0.0
INCIDENT_BEAM_DIRECTION=0.0 0.0 1.0
FRACTION_OF_POLARIZATION=0.99 ! SLS X06SA
POLARIZATION_PLANE_NORMAL= 0.0 1.0 0.0
DETECTOR=CCDCHESS    MINIMUM_VALID_PIXEL_VALUE=0     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 1.35    !Relative radius limiting trusted region on detector
VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= 6000 30000 !Used by DEFPIX
INCLUDE_RESOLUTION_RANGE=50.0 2.6 !Angstroem; used by DEFPIX,INTEGRATE,CORRECT

The statistics of the merged dataset (comprising ms424_2, ms424_3 and ms424_4) may be found in table S1 of [1].