2GIF: Difference between revisions
Jump to navigation
Jump to search
mNo edit summary |
mNo edit summary |
||
| (5 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
== Structural asymmetry of AcrB trimer suggests a peristaltic pump mechanism == | == Structural asymmetry of AcrB trimer suggests a peristaltic pump mechanism == | ||
The structure of AcrB was solved by molecular replacement, followed by many cycles of refinement and model building. The raw data are available at | 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 https://{{SERVERNAME}}/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 | 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 | ||
| Line 7: | Line 7: | ||
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. | 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 ms424_2 may be found in table S1 of [http://strucbio.biologie.uni-konstanz.de/strucbio/files/Seeger_Science_313_1295_SOM.pdf]. | |||
Latest revision as of 18:22, 24 March 2020
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 https://wiki.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 ms424_2 may be found in table S1 of [1].