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OASIS

OASIS. • What is it? • How it works? • What next?. Two categories of Direct Methods in Protein Crystallography. Ab initio direct methods : SnB (H.A. Hauptman’s team) ShelxD (G.M. Sheldrick’s team) Acorn (M.M. Woolfson’s team). OASIS

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OASIS

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  1. OASIS • What is it? • How it works? • What next?

  2. Two categories of Direct Methods in Protein Crystallography Ab initio direct methods: SnB (H.A. Hauptman’s team) ShelxD (G.M. Sheldrick’s team) Acorn (M.M. Woolfson’s team) OASIS A program of direct-method phasing based on a partial model with or without SAD/SIR information

  3. Features • Phase derivation based on a partial model with or without SAD/SIR information • breaking the SAD/SIR phase ambiguity • phase flipping of the partial model • SAD/SIR iteration iterative SAD/SIR phasing and model building •MR iteration iterative phasing and model building without using SAD/SIR information

  4. OASIS • What it is? • How it works? • What next?

  5. Breaking the SAD phase ambiguity TT0570(2d5w)sulfur-SAD CuKa data, redundancy = 26.1 (1206 resides in the AU,Bijvoet ratio = 0.55%) Programs used: Oasis, DM, FFT program in CCP4 and PyMOL Chinese Physics B 17, 1-9 (2008)

  6. ARP/wARP2.0 Å Buccaneer 2.5 Å Final 2.2 Å Buccaneer3.0 Å Iterative SAD phasing & model building TT0570(2d5w)sulfur-SAD CuKa data Programs used: Oasis, DM, Resolve (build only), RefMac and ARP/wARP or Buccaneer

  7. Dual-space SAD/SIR iteration Acta Cryst. D60, 1991-1996 (2004) Acta Cryst. D62, 883-890 (2006)

  8. |Fo|exp(ij)Þr(r) Reciprocal space： Replacing |Fc| with |Fo| andmodifying j Real space： modifying r(r) |Fc|exp(ij)Ür(r) Dual-space iteration - a phasing framework

  9. Dual-space iterative phasing Gerchberg, R.W. & Saxton, W.O. Optik, 34, 275-284 (1971)；35, 237-246 (1972) Wang, B.C. Methods in Enzymology 115, 90-112 (1985) Weeks, C. M., Detita, G. T., Miller, R. & Hauptman, H. A. Acta Cryst. D49, 179-181 (1993) Sheldrick, G. M., Hauptman, H. A., Weeks, C. M., Miller, R. & Usoâ N, I. (2001). International Tables for Crystallography Vol. F, edited by E. Arnold & M. Rossmann, pp. 333-351. Wang, J.W., Chen, J. R., Gu, Y. X., Zheng, C. D. & Fan, H. F. Acta Cryst. D60, 1991–1996 (2004) SAD/SIR phasing + model completion (fragment extension)

  10. Dual-space MR iteration Acta Cryst. D63, 793-799 (2007)

  11. MR model Final model 46 residues 13 with side chains 215 residues MR-model completion with E7_C–Im7_C data (1ujz) OASIS-DM-ARP/wARP iteration E7_C–Im7_C Cycle 7 Cycle 5 Cycle 1 Cycle 3 201 residues all with side chains ARP/wARP-DM iteration Cycle 2 Cycle 1

  12. Flipping 范海福 《物理学报》21, 1105-1113 (1965) (in Chinese) Hai-fu Fan, Chinese Phys. 1418-1428 (1965) Sign flipping Weeks, C. M., Detita, G. T., Miller, R. & Hauptman, H. A. Acta Cryst. D49, 179-181 (1993) Phase flipping Sheldrick, G. M., Hauptman, H. A., Weeks, C. M., Miller, R. & Usoâ N, I. (2001). International Tables for Crystallography Vol. F, edited by E. Arnold & M. Rossmann, pp. 333-351 Atom flipping Oszlányi, G. & Sütő, A. Acta Cryst. A60, 134-141 (2004) Charge flipping He, Y., Yao, D.Q., Gu, Y. X., Lin, Z.J., Zheng, C. D. & Fan, H. F. Acta Cryst. D63, 793-799 (2007) Phase flipping

  13. Examples on model completion by the program combination of OASIS(phasing) DM(density modification) Buccaneer(model building) RefMac(refinement) with starting models from different program packages without involving OASIS

  14. Model resulting from SAD phasing MR iteration based on a SAD model Tom70p (2gw1) 3.3Å Se-SAD data, redundancy = 3.3 MR iteration Oasis - DM - Buccaneer - Refmac Final 1086 residues in the AU

  15. MR-iteration based on a MAD model Set9/7 (1h3i) 2.8Å data MAD model extended after 7 cycles iteration of Oasis - DM - Buccaneer - Refmac Model resulting from MAD phasing Final 586 residues in the AU

  16. MR-iteration based on an MIR model Rpe (1lia) 2.8Å data Final 668 residues in the AU MIR model extended after 9 cycles of Oasis - DM - Buccaneer - Refmac Model resulting from MIR phasing

  17. Model resulting from MRSAD phasing MR iteration based on anMRSAD model TM1782 (1vkn) 1.8Å Se-SAD data, redundancy = 6.1 MR iteration Oasis - DM - Buccaneer - Refmac Final 1356 residues in the AU

  18. Model resulting from MRSAD phasing MR iteration based on anMRSAD model TM0119 (2f4l) 2.5Å Se-SAD data, redundancy = 3.8 MR iteration Oasis - DM - Buccaneer - Refmac Final 1140 residues in the AU

  19. What next? • Further improve the phasing algorithm • Allow using a rough electron density map instead of a partial model during the iteration • Combine oversampling procedure with direct-method phasing

  20. Acknowledgements Professor Quan Hao University of Hong Kong, China Professor Yuan-xin Gu, Dr. Jia-wei Wang, Dr. Yao He, Dr.Tao Zhang Institute of Physics, Chinese Academy of Sciences, Beijing, China ProfessorZheng-jiong Lin, Dr. Qiu-ying Yang Institute of Biophysics, Chinese Academy of Sciences,Beijing China Dr. Santosh Panjikar EMBL-Hamburg Outstation, Hamburg, Germany The project is supported by the Chinese Academy of Sciences and the 973 Project (Grant No. 2002CB713801) of the Ministry of Science and Technology of China.

  21. Thank you!

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