JCSG Data Archives


JCSG Repository of Crystallographic Datasets

 

The Joint Center for Structural Genomics has created a unique repository of X-ray crystallographic datasets for the structures that it has solved and deposited in the Protein Data Bank. This archive contains the experimental data and analyses from the data collection, data reduction, phasing, density modification, model building and refinement of JCSG structures. It also includes full sets of diffraction images for each of our deposited structures, enabling complete reconstruction of the data processing. In most cases, phasing was carried out either by SeMet, MAD or Molecular Replacement.   These datasets are freely available to the scientific community for developing and testing new algorithms and benchmarking and teaching.

 

In order to register, please contact Ashley Deacon:
    by phone (650) 926 5108 or
    by email adeacon@slac.stanford.edu.
 
If you are already a registered user go to structure gallery

 

References listing research and development that has benefited from the use of our repository

  1. Cowtan K (2006) The Buccaneer software for automated model building. 1. Tracing protein chains. Acta Cryst D62:1002-11.
  2. Sauter NK, Grosse-Kunstleve RW, Adams PD (2006) Improved statistics for determining the Patterson symmetry from unmerged diffraction intensities. J Appl Cryst 39:158-68.
  3. Yao JX, Dodson EJ, Wilson KS, Woolfson MM (2006) ACORN: a review. Acta Cryst D62:901-8.
  4. Cowtan K. Fitting molecular fragments into electron density. Acta Cryst D. 2008;64:83-9.
  5. Faust A, Panjikar S, Mueller U, Parthasarathy V, Schmidt A, Lamzin VS, et al. (2008) A tutorial for learning and teaching macromolecular crystallography. J Appl Cryst. 41:1172.
  6. Joosten RP, Womack T, Vriend G, Bricogne G (2009). Re-refinement from deposited X-ray data can deliver improved models for most PDB entries. Acta Cryst D65:176-85.
  7. Panjikar S, Parthasarathy V, Lamzin VS, Weiss MS, Tucker PA (2009) On the combination of molecular replacement and single-wavelength anomalous diffraction phasing for automated structure determination. Acta Cryst D65:1089-97.
  8. Sauter NK, Zwart PH (2009) Autoindexing the diffraction patterns from crystals with a pseudotranslation. Acta Cryst D65:553-9.
  9. Skubak P, Murshudov G, Pannu NS (2009) A multivariate likelihood SIRAS function for phasing and model refinement. Acta Cryst D65:1051-61.
  10. Terwilliger TC, Adams PD, Read RJ, McCoy AJ, Moriarty NW, Grosse-Kunstleve RW, et al.(2009) Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard. Acta Cryst D65:582-601.
  11. Winter G (2005). Application of automation to data processing & analysis. CCP4 Newsletter on Protein Crystallography No. 43.
  12. Poon BK, Grosse-Kunstleve RW, Zwart PH, Sauter NK (2010) Detection and correction of underassigned rotational symmetry prior to structure deposition. Acta Cryst D66:503–513.
  13. M. Cymborowski, M. Klimecka, M. Chruszcz, M. D. Zimmerman, I. A. Shumilin, D. Borek, K. Lazarski, A. Joachimiak, Z. Otwinowski, W. Anderson, and W. Minor (2010) To automate or not to automate: this is the question J Struct Funct Genomics 11: 211–221.
  14. G. Winter (2010) xia2: an expert system for macromolecular crystallography data reduction J Appl Cryst 43:186-190
  15. Diederichs K (2010) Quantifying instrument errors in macromolecular X-ray data sets Acta Cryst D66: 733-740
  16. Sauter NK, Poon BK (2010) Autoindexing with outlier rejection and identification of superimposed lattices J. Appl. Cryst. (2010). 43, 611-616
  17. Pavelcík F , Václavík J (2010) Performance of phased rotation, conformation and translation function: accurate protein model building with tripeptidic and tetrapeptidic fragments Acta Cryst. D66, 1012-1023
  18. Skubák P, Waterreus W-J,  Pannu NS (2010) Multivariate phase combination improves automated crystallographic model building Acta Cryst. D66, 783-788
  19. Cowtan K (2010)  Recent developments in classical density modification. Acta Cryst D66: 470-478.