The structure of KdnA was determined via molecular replacement using the software package PHASER,11 (link) with the coordinates of QdtB serving as the search model.12 (link) 4-fold averaging and solvent flattening yielded an electron density map that allowed for essentially a complete tracing of the KdnA polypeptide chain. The model was subjected to alternate cycles of refinement with REFMAC13 (link) and manual model building with COOT.14 (link),15 (link) KdnB was also solved using PHASER with the search model being that of PDB entry 3RF7. The KdnB model was refined in a similar manner as that for KdnA. Model refinement statistics are listed in
Structural Determination of KdnA and KdnB
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Other organizations : University of Wisconsin–Madison
Variable analysis
- X-ray data sets collection method using a Bruker AXS Platinum 135 CCD detector controlled with the Proteum software suite
- X-ray source (Cu Kα radiation from a Rigaku RU200 X-ray generator equipped with Montel optics) operated at 50 kV and 90 mA
- X-ray data sets processing with SAINT and scaling with SADABS
- Electron density map generated from 4-fold averaging and solvent flattening
- Refined KdnA and KdnB models
- Rigaku RU200 X-ray generator
- Bruker AXS Platinum 135 CCD detector
- Proteum software suite
- SAINT and SADABS software for X-ray data processing
- PHASER software for molecular replacement
- REFMAC software for model refinement
- COOT software for manual model building
- QdtB coordinates used as the search model for molecular replacement to determine the structure of KdnA
- PDB entry 3RF7 used as the search model for molecular replacement to determine the structure of KdnB
- Not explicitly mentioned
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