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Remember, that MPD is chiral, so you have two possibilities at C4. After putting MPD into your model the FoFc-density should clearly tell you (your resolution looks better than 2 A), if the group on the left in your picture is a phosphate / sulfate or if it only has a carbon in the middle of the tetrahedrally bound atom. Check for hydrogen bonding partners, which help to identify hydroxy groups. greetings Gottfried At Wednesday, 17-07-2013 on 06:14 sonali dhindwal wrote: hi Wei, This looks like MPD, 2-Methyl-2,4-pentanediol. May b u have added it as ur cryo-protectant. Thanks and Regards -- Sonali Dhindwal “Live as if you were to die tomorrow. Learn as if you were to live forever.” ------------------------- From: sonali dhindwal To: "[log in to unmask]" Sent: Wednesday, 17 July 2013 9:44 AM Subject: Re: [ccp4bb] Dose anyone see this ligand before? hi Wei, This looks like MPD, 2-Methyl-2,4-pentanediol. May b u have added it as ur cryo-protectant. Thanks and Regards -- Sonali Dhindwal “Live as if you were to die tomorrow. Learn as if you were to live forever.” ------------------------- From: Wei Feng To: [log in to unmask] Sent: Tuesday, 16 July 2013 9:05 PM Subject: [ccp4bb] Dose anyone see this ligand before? Dear all, I found some redundant density in my structure beween two molecule. (see picture 1 and 2) But I am not sure which ligand will be. Dose everyone see this ligand before? If so, can you tell the PDB code or send me the struture file? Thank you for your time! Wei