Protein Science (2016) 25(3): 720-33. DOI: 10.1002/pro.2861

Protein purification and crystallization artifacts: the tale usually not told
Ewa Niedzialkowska, Olga Gasiorowska, Katarzyna B. Handing, Karolina A. Majorek, Przemyslaw J. Porebski, Ivan G. Shabalin, Ewelina Zasadzinska, Marcin Cymborowski, Wladek Minor


MR can be successfully used to identify crystallization artifacts

Overview of MR experiments run with diffraction data collected from crystallization artifacts: Sigma70 (YodA), GNAT (YodA) and xSix (YadF) and from NYSGC target 021790 as a control. The codes presented here were used as a templates for MR. Resulting overall R factor <= 0.30 colored in green. Missing values indicate that MOLREP was not able to find any solution.

      MR overall Rfactor      
Name of protein PDB ID MW [kDa] Sigma70 (YodA) GNAT (YodA) xSix (YadF) 021790 (control)
Metal-binding lipocalin(YodA) 1OEJ 24.5 0.28 0.24 0.54 0.55
  1OEE 22.3 0.29 0.26 0.56 0.55
  4TNN 24.5 0.24 0.30 0.56 -
  1S7D 24.8 0.28 0.24 0.55 0.54
  1TXL 24.6 0.29 0.25 0.55 0.54
Carbonic dehydratase (YadF) 1T75 25.1 0.54 0.52 0.21 0.55
  3QY1 25.1 0.54 0.52 0.22 0.55
  1I6O 27.2 0.54 0.51 0.22 0.54
  1I6P 27.2 0.54 0.52 0.2 0.54
Ferric uptake regulator (Fur) 2FU4 9.33 0.53 0.51 0.55 0.55
cAMP-regulatory protein (CRP) 2GZW 23.51 0.55 0.51 0.52 0.54
Glucosamine-6-phosphate synthase (GlmS) 1MOQ 40.31 - 0.53 - 0.54
  2J6H 66.76 - 0.55 - 0.55
  4AMV 66.86 - 0.55 - 0.55
Glycogen synthase (GlgA) 2QZS 53.89 - 0.54 - 0.55
Component 1 of the 2-oxoglutarate dehydrogenase complex (ODO1) 2JGD 105.03 - - - 0.56
Component E2 of the dihydrolipoamide succinyl transferase (ODO2) 1E2O 26.07 0.53 0.52 0.55 0.54
Formyl transferase (YfbG) 2BLN 33.21 0.54 0.52 0.56 0.55
  1YRW 32.83 0.54 0.53 0.56 -
  2BLL 40 0.54 0.53 - 0.55
Cu/Zn-superoxide dismutase (Cu/Zn-SODM) 1ESO 15.74 0.53 0.51 - 0.54
Chloramphenicol-O-acetyl transferase (CAT) 3U9F 25.66 0.52 0.52 0.55 0.54
  1PD5 25.66 0.53 0.51 0.56 0.54
Hsp60 4AAR 57.28 - 0.55 - 0.55
Host factor-I protein (Hfq) 4PNO 8.12 0.54 0.52 0.54 0.55
  2YHT 8.25 0.53 0.52 - 0.55
Maltose-binding protein (MBP) 1PEB 40.06 - 0.54 - 0.54
  1NL5 40.06 0.54 0.52 - 0.54
  1ZJL 40.06 0.55 0.52 - 0.55
  1ZIU 40.06 - 0.53 - 0.55
N-Utilization substance (NusA) 2CXC 16.04 0.53 0.51 - 0.54
  1U9L 7.77 0.53 0.52 0.53 0.55
  1L2F 40.9 0.54 0.53 - 0.54
  1K0R 39.81 0.55 0.51 0.55 0.54