Solving Crystal Structures A tiny team in the Institute of Physics dedicated to Methods of Solving Crystal Structures http://cryst.iphy.ac.cn

Our target is the phase problem in X-ray Crystallography and Electron microscopy The application field of our research outcome covers Material Science and Life Science

Road Map

X-ray crystallography Electron microscopy Acting as a tool of image processing Direct methods Dealing with pseudo symmetries Pseudo centro symmetry Pseudo translational symmetries Two-stage image processing Enantiomorphous phase ambiguity Translational phase ambiguity Direct determination of modulated structures from electron diffraction data Phasing protein OAS and SIR data Ab initio solution of superstructures Ab initio solution of incommensurate and composite structures

Freely available at http://cryst.iphy.ac.cn Our products SAPI (1985 – 1995) DIMS (1994 – 1997) VEC (1995 – 2000) OASIS (2000 – ) (1985 – 1995) (1994 – 1997) (1995 – 2000) (2000 – 20??) Freely available at http://cryst.iphy.ac.cn

The program VEC More than 1000 copies of the program have been distributed in 66 countries/areas

Original EM from Prof. N. Uyeda Symmetry averaging ED from Prof. N. Uyeda Original EM from Prof. N. Uyeda Two-Step Image Processing Image Decon- volution Phase extension Fourier recycling Search for defocus Partial structure model Complete

Image Processing of Bi-2212 Deconvolution FT-1 Phase extension Space group: N [Bbmb] 1 -1 1 a = 5.42, b = 5.44, c = 30.5Å q = 0.21b* + c* EM image courtesy of Dr. S. Horiuchi Deconvolution FT-1 c b Bi Sr Cu Ca Oxygen in Cu-O layer Phase extension

OASIS-2004 A direct-method program for ab initio phasing and reciprocal-space fragment extension with SAD/SIR data

Features: Product of Cochran and Sim distributions rather than the Sim distribution alone is used for discrimination of experimental bimodal SAD distribution; Auto scaled coefficient taking account of experimental lack-of-closure error is introduced to the direct-method phasing formula; Reciprocal-space fragment extension is made possible by feeding back partial-structure information to the direct-method phasing. The combination of OASIS-2004, DM, RESOLVE (build only) and ARP/wARP can perform a dual-space fragment extension. This enables a fragment as small as ~20% to be automatically expanded to more than 95% of the complete structure.

Dual-space fragment extension Partial model No Yes Reciprocal-space fragment extension by OASIS-2004 + DM Real-space RESOLVE BUILD and/or ARP/wARP OK? End

OASIS-2004 application Xylanase Contoured at 1s Space group: P21 Unit cell: a = 41.07, b = 67.14, c = 50.81Å b = 113.5o 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% Phasing: OASIS-2004 + DM (Cowtan) Model building: RESOLVE BUILD & ARP/wARP found 299 of the total 303 residues at the 6th cycle of iteration Data courtesy of Dr. Z. Dauter, National Cancer Institute, USA

OASIS-DM-(RESOLVE BUILD, ARP/wARP) Iteration - Partial model from RESOLVE BUILD or ARP/wARP Phase error in degrees 70 60 50 40 30 20 80 10 Cycle 5 1 6 2 4 3 OASIS-DM-(RESOLVE BUILD, ARP/wARP) Iteration Xylanase sulfur-SAD phasing Synchrotron radiation l = 1.49Å, <DF>/<F> = 0.56% Is OASIS-2004 necessary?

Improvement on electron-density map and automatic model building Cycle 0 Cycle 3 Cycle 6 Improvement on electron-density map and automatic model building

TT0570 OASIS-2004 application Space group: P21212 Unit cell: Data courtesy of Professor Isao Tanaka & Dr. Nobuhisa Watanabe Graduate School of Science, Hokkaido University, Japan Space group: P21212 Unit cell: a = 100.2639 b = 108.9852 c = 114.6272Å Number of residues in the ASU: 1206 Resolution range: 50.00-2.01Å Multiplicity: 20.9 Anomalous scatterer: S (22) Wavelength: l = 2.291Å; Df ” = 1.14 Bijvoet ratio: <|DF|>/<F> = 1.16% Phasing: OASIS-2004 + DM (Cowtan) Model building: RESOLVE BUILD & ARP/wARP ARP/wARP found 1153 of the total 1206 residues after 2 cycles of iteration OASIS-2004 application

My colleagues (last 5 years): Prof. Gu, Yuan-xin Prof. Zheng, Chao-de Mr. He, Yao Mr. Yao, De-qiang Dr. Hao, Quan Dr. Chen, Jian-rong Dr. Wang, Jia-wei Dr. Huang, sheng

Thank you!