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What is it?

ContaMiner is a rapid automated large-scale detection of contaminant crystals.

Protein contaminants, from the expression host, purification buffers or from the affinity tags used, may crystallise instead of a protein of interest. Unfortunately, this only becomes clear once the crystal structure has been determined...

ContaMiner allows rapid screening of X-ray diffraction data against the most likely proteins contaminants.

How does it work?

Given an mtz or cif data file, ContaMiner uses an optimized molecular replacement procedure, based on the MoRDa automatic molecular replacement pipeline. Contaminants tested include 43 Proteins in E.coli, 2 Proteins in yeast, 8 Tags, 16 Proteins used during purification or crystallization, 4 Microbial contaminants of host cell and reagents and 4 From other expression systems. The full list is available here. Any additional suggestions or comments? -- Please let us know.

Why should I use it?

Possible benefits of using ContaMiner may include not wasting your time for solving that chloramphenicol acetyltransferase crystal, or reassuring reviewers and yourself that your Crystallisation and Preliminary X-ray Analysis paper does not report, in fact, another structure of MBP.

How to use it?

  1. Choose an optional name for your task. If not given, the default name is the name of the uploaded file.
  2. Upload your structure file.
  3. Indicate your email address to receive a message when your task is completed. If you are logged in, your email address is used by default.
  4. To speed up the procedure, select only likely added contaminants in the dedicated tab.
The ouput is easy to read. Names refer to Uniprot identifiers. Click on the identifiers to obtain MoRDa statistics.

Colour code:

If ContaMiner gives you a positive result, you are encouraged to check if the submitted dataset is of significantly higher resolution as the currently available MR template. This case might justify deposition of you model and data at the PDB.

How to cite ContaMiner and/or ContaBase?

To cite ContaMiner and/or ContaBase, please use:
Hungler A, Momin A, Diederichs K, Arold ST (2016)
ContaMiner and ContaBase: a web server and database for early identification of unwantedly crystallized protein contaminants
J. Appl. Cryst. 49, 2252-2258
Read it here

ContaMiner heavily relies on MoRDa. We therefore recommend to also cite:

Vagin A. & Lebedev A (2015)
MoRDa, an automatic molecular replacement pipeline
Acta Cryst. A71, s19
Read it here

It's your turn

Submitting anisotropically cut data can produce false positives, because of possible anomalies within certain CCP4 programs. Use with care!

Proteins in E.coli

Proteins in yeast


Proteins used during purification or crystallization

Microbial contaminants of host cell and reagents

From other expression systems

Do it by yourself

If you want to run ContaMiner on your own cluster, you can download it here.