Refinement with ligands and covalent links

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1. Using links available from CCP4 dictionary

Description:
Adding glycan to a protein crystal structure and refinement of the completed structure

Project directory:         jligand/1_glycan/
Reflection data:            4gos.mtz
Incomplete structure:   model.pdb

Details
Check your results

2. Using a new ligand description

Description:
Refinement of a new structure from the PDB that contains a ligand missing in the CCP4 dictionary

Project directory:         jligand/2_newligand/
Reflection data:            4do4.mtz
Structure:                     4do4.pdb

Details

3. Using a new ligand and link descriptions

Description:
Additional dictionary is generated defining two entries:
– covalent link between PLP and LYS and
– isolated ligand formed by covalently bound PLP and Methyl-ASP
A structure containing two forms of bound PLP is completed and refined.

Project directory:         jligand/3_newlink/
Reflection data:            1ajs.mtz
Incomplete structure:   model.pdb

Details

Related web resources

Ligand Expo at RCSB PDB
http://ligand-expo.rcsb.org/

The PRODRG Server
http://davapc1.bioch.dundee.ac.uk/prodrg/