The crystals belong to space group R32 with unit cell dimensions a = b = 114.0 Å and c = 307.0 Å approximately. The apo structure was determined by molecular replacement with MOLREP37 (link) using the GP structure of the GP-KZ52 Fab complex (PDB ID, 3CSY) as a search model. There is one GP molecule in the crystal asymmetric unit. The biological trimer is formed by a crystallographic 3-fold axis. Structure refinement used REFMAC38 (link) and models were rebuilt with COOT39 (link). The apo structure was refined to 2.23 Å resolution with an Rwork of 0.223 (Rfree, 0.251) and good stereochemistry. Close examination of the data from inhibitor soaked crystals showed that only toremifene and ibuprofen were fully bound with GP, and structures were refined to resolutions of 2.69 Å and 2.68 Å, respectively. 4-hydroxyltamoxifen was only bound with partial occupancy (data not shown). Data collection and structure refinement statistics are given in Table 1. Structural comparisons used SHP40 (link), figures were prepared with PyMOL41 .
Cryo-Crystallography of Glycoprotein Inhibitors
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Corresponding Organization : Diamond Light Source
Other organizations : University of Oxford, Wellcome Centre for Human Genetics
Protocol cited in 8 other protocols
Variable analysis
- Concentration of crystallization liquor or inhibitor soaking solution used for cryo-protection (75% v/v)
- Concentration of glycerol used for cryo-protection (25% v/v)
- Inhibitors soaked (toremifene, tamoxifen, 4-hydroxyltamoxifen, raloxifene, clomiphene, ibuprofen, benztropine)
- Diffraction resolution of crystals
- Binding of inhibitors to the GP molecule
- Temperature of data collection (100 K)
- Detectors used (PILATUS 6M)
- Beamlines used (I03 for native data, I02 for inhibitor soaked crystals)
- Exposure time per diffraction image (0.1 s for native data, 0.05 s for inhibitor soaked crystals)
- Beam size (80×20 μm for native data, 90×25 μm for inhibitor soaked crystals)
- Beam transmission (30% for native data, 40% for inhibitor soaked crystals)
- Space group of crystals (R32)
- Unit cell dimensions (a = b = 114.0 Å, c = 307.0 Å)
- Search model used for molecular replacement (GP structure of the GP-KZ52 Fab complex, PDB ID 3CSY)
- Refinement methods (REFMAC, COOT)
- Positive control: Not mentioned
- Negative control: Not mentioned
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