Computational protocol: Architecture and hydration of the arginine‐binding site of neuropilin‐1

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Protocol publication

[…] X‐ray diffraction data were collected at 100 K on beamline I04 at the Diamond Light Source, Didcot UK. All data sets were processed with xia2‐3d automated software system , , , , . Molecular replacement solutions were obtained by Phaser using an apo NRP1‐b1 domain (PDB code 1KEX) as the search model. The refinement was carried out by Refmac5 . The dictionary files for the fragments were generated using the acedgr programme from ccp4 software suite . Iterative rounds of building and refinement were carried out in COOT and Refmac5. TLS (Translation/Libration/Screw) groups were generated automatically by Refmac5. Data collection and refinement statistics for all structures can be found in Table . […]

Pipeline specifications

Software tools xia2, REFMAC5, CCP4, Coot
Applications Small-angle scattering, Protein structure analysis
Diseases Neoplasms
Chemicals Tyrosine