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International Conference on Structural Genomics 2006 Hands-on Workshop III

International Conference on Structural Genomics 2006 Hands-on Workshop III. Automated Structural Determination by X-ray Crystallography. Yokohama, Japan October 19-20, 2006. OASIS-2006. Institute of Physics Chinese Academy of Sciences Beijing 100080, P.R. China.

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International Conference on Structural Genomics 2006 Hands-on Workshop III

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  1. International Conference on Structural Genomics 2006 Hands-on Workshop III Automated Structural Determination by X-ray Crystallography Yokohama, Japan October 19-20, 2006

  2. OASIS-2006 Institute of Physics Chinese Academy of Sciences Beijing 100080, P.R. China http://cryst.iphy.ac.cn

  3. in CCP4 OASIS (2000) OASIS-2004 on the Web OASIS-2006 on the Web soon

  4. OASIS-2006 GUI for CCP4i

  5. Functions ofOASIS 1. Direct-method 2. Reciprocal-space Dual-space Fragment Extension by combining with DM, RESOLVE and ARP/wARP SAD/SIR Phasing Fragment Extension

  6. Why direct methods? For better initialSAD phases!

  7. Bimodal distribution from SAD Cochran distribution Sim distribution Peaked at Peaked at any where from 0 to2p The phase of F” Phase information available in SAD

  8. Sim-modified phases PSim PBimodal PSim PCochran P+ P + P+ P+-modified phases Two different kinds of initial SAD phases

  9. Comparisonof 4 typical reflections from the protein histone methyltransferase SET 7/9

  10. Histone methyltransferase SET 7/9 Comparison of cumulative phase errors in descendingorder ofFobs Number of reflections Errors of Sim-modified phases (o) Errors of P+-modified phases (o) 1500 57.1 45.8 3000 57.1 49.1 4500 56.5 50.0 6000 57.0 51.2 7500 57. 8 52.9 9000 58.7 54.1 10500 59.4 55.6 12000 60.8 56.9 13500 61.9 58.4 15000 63.4 60.2 16352 65.2 62.3

  11. Why dual-space? For less systematic errors!

  12. Dual-space fragment extension Real-space fragment extension RESOLVE BUILD and/or ARP/wARP Reciprocal-space fragment extension OASIS + DM Partial model OK? No Yes End Partial structure

  13. OASIS Applications

  14. Ab initio SAD phasing with weak anomalous signal

  15. OASIS-DM-RESOLVE BUILD cycle 0 25% OASIS-DM-ARP/wARP cycle 6 99% SHARP-DM-RESOLVE BUILD SHARP-SOLOMON-ARP/wARP BP3-DM-RESOLVE BUILD Xylanase Space group: P21 Unit cell: a = 41.07, b = 67.14, c = 50.81Å b = 113.5o Number of residues in the ASU: 303 Resolution limit: 1.75Å; Multiplicity: 15.9 Anomalous scatterer: S(5 ) X-rays:synchrotron radiation l = 1.488Å; D f ” = 0.52 Bijvoet ratio:<|DF |>/<F > = 0.56% Data courtesy of Dr. Z. Dauter, National Cancer Institute, USA

  16. SAD phasing at different resolutions TT0570 Cu-Ka data, <|DF|>/<F> ~ 0.55% 3.5Å 2.1Å 4.0Å

  17. SOLVE/RESOLVE results improved by OASIS + DM

  18. Dual-space fragment extensionbased on SOLVE/RESOLVE results 1LIA (d14)2.8Å SIR data SOLVE/RESOLVE + OASIS-DM-RESOLVE (BUILD) SOLVE/RESOLVE

  19. Dual-space fragment extensionbased on SOLVE/RESOLVE results 2GW1 3.3Å SAD data Sigma_A map based on a model manually built from the SOLVE/RESOLVE map SOLVE/RESOLVE map OASIS-DM map based on the same model

  20. SOLVE/RESOLVE map OASIS-DM map based on the same model Sigma_A map based on a model manually built from the SOLVE/RESOLVE map Dual-space fragment extensionbased on SOLVE/RESOLVE results 2GW1 3.3Å SAD data

  21. Fragment extension based on Molecular Replacement

  22. ARP/wARP-OASIS-DMiteration Final model ARP/wARP-DM iteration MR model Cycle 2 Cycle 3 Cycle 1 acidic phospholipase A2 124 residues 48 residues 60 residues Cycle 11 Cycle 9 Cycle 13 ARP/wARP-DM iteration Fragment extension based on molecular replacement

  23. A difficult case:1UJZ Space group: I 222 Unit cell: a=62.88, b=74.55, c=120.44Å Number of residues in ASU: 215 molecule A: 87 residues molecule B: 128 residues Number of residues in the starting model: 46 (all in Mol. A) Resolution range: 37.57 – 2.10Å Number of reflections: 16460

  24. Dual-space Fragment Extension without SAD/SIR information

  25. Yes No Model rebuild by RESOLVE BUILD or ARP/wARP Density modification by DM Phase improvement by OASIS MR model OK? Partial structure End

  26. P+ > 0.5 j” + Dj = jmodel <|Dj|> ~ 90o <2|Dj|> ~ 180o |Dj| j” |Dj| • P+ < 0.5 • j” - Dj • jmodel - 2|Dj|

  27. 1UJZ Phase Statistics

  28. ARP/wARP-OASIS-DM iteration Cycle 7 Cycle 5 Cycle 1 Cycle 3 201 residues all with side chains MR model Final model 46 residues 13 with side chains 215 residues ARP/wARP-DM iteration Cycle 2 Cycle 1

  29. Participants of this project Staffs Hai-fu Fan1, Yuan-xin Gu1, Tao Jiang2, Zheng-jiong Lin2 & Chao-de Zheng1 Ph.D. students Jian-rong Chen1, Qiang Chen3, Yao He1, Sheng Huang1,4, He Li2, Jia-wei Wang1, Li-jie Wu1, De-qiang Yao1,5 & Tao Zhang1,6 1 Institute of Physics, CAS, Beijing, China 2 Institute of Biophysics, CAS, Beijing, China 3 Peking University, Beijing, China 4 Institute of High Energy Physics, CAS, Beijing, China 5 Univ. of Science & Technology of China, Hefei, China 6 Lanzhou University, Lanzhou, China

  30. Acknowledgements SAD data used in this presentation were kindly provided by Dr. Z. Dauter1, Dr. S. J. Gamblin2, Dr. B. D. Sha3, Prof. I. Tanaka4, Dr. N. Watanabe4 & Dr. B. Xiao2 1 Argonne National Laboratory, USA 2 The National Institute for Medical Research, UK 3 Department of Cell Biology, University of Alabama at Birmingham, USA 4 Graduate School of Science, Hokkaido University, Japan

  31. Thank you!

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