There are two option in Database >Set quotas>
1.One is Set database Quota to 1024 MB.
2.Other one is Set warning threshold to 900 MB.
Here first option is for increase quota & other one for warns to user,that there are no enough space for him.You have to increse the value here also.Check it you have not changed the value here.
For Example :
1.One is Set database Quota to 2048 MB.
2.Other one is Set warning threshold to 2000 MB.
Or, You can replicate the mails for the user, make a local NSF in your Local HDD & delete the mails from server & run Load compact .Hope ,it will help you..