1. OASIS-2004 Institute of Physics, CAS, Beijing, P.R. China http://cryst.iphy.ac.cn A direct-method program for ab initio phasing and reciprocal-space fragment extension with SAD/SIR data

2. People who contributed to the demonstration People who contributed to the demonstration Yuan-xin Gu, Cheng Yang, Jia-wei Wang, Sheng Huang De-qiang Yao & Hai-fu Fan

3. OASIS-2004 application Contoured at 1  Xylanase Space group: P2 1 Unit cell: a = 41.07, b = 67.14, c = 50.81Å  = 113.5 o Resolution limit: 1.75Å; Multiplicity: 15.9 Anomalous scatterer: S (5 ) X-rays:  synchrotron radiation  = 1.488Å;  f ” = 0.52 Bijvoet ratio: / = 0.56% Phasing: OASIS-2004 + DM (Cowtan) Model building: RESOLVE BUILD & ARP/wARP found 299 of the total 303 residues at the 6 th cycle of iteration Data courtesy of Dr. Z. Dauter, National Cancer Institute, USA

4. TT0570 Data courtesy of Professor Isao Tanaka & Dr. Nobuhisa Watanabe Graduate School of Science, Hokkaido University, Japan Space group: P2 1 2 1 2 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: = 2.291Å;  f ” = 1.14 Bijvoet ratio: / = 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

5. 1. Better initial SAD phases

6. Bimodal distribution of SAD The phase of F” Phase information available in SAD Cochran distribution Peaked at any where from 0 to 2  Peaked at Sim distribution

7. Two different kinds of initial SAD phases P+P+ + P P Sim P Bimodal Sim-modified phases P + -modified phases P+P+ P Sim P Cochran

8. Se-SAD Histone Methyltransferase Set 7/9 Space group: P2 1 2 1 2 1 Unit cell: a = 66.09, b = 82.83, c = 116.15Å Number of residues in ASU: 560 Number of independent reflections: 16352 Resolution limit: 2.8Å Multiplicity: 3.8 Anomalous scatterer: Se(12)  = 0.9794Å;  f’ = -7.5,  f” = 6.5 Bijvoet ratio: / = 7.03% SAD phasing by OASIS-2004 + DM Data provided by Dr. S. J. Gamblin and Dr. B. Xiao Cover figure of Acta Cryst. D60, Part 11 (2004)

9. Comparison of the two types of initial phases using 4 typical reflections from the protein histone methyltransferase SET 7/9

10. Comparison on cumulative phase errors sorted in descending order of F obs Comparison on cumulative phase errors sorted in descending order of F obs 60.263.415000 58.461.913500 56.960.812000 62.365.216352 55.659.410500 54.158.79000 52.957. 87500 51.257.06000 50.056.54500 49.157.13000 45.857.11500 Errors of P + -modified phases ( o ) Number of reflections Errors of Sim-modified phases ( o )

11. 2. Inclusion and auto balance of the lack-of-closure error in the direct-method phasing formula 2. Inclusion and auto balance of the lack-of-closure error in the direct-method phasing formula

12. Automatic solution of protein structures OASIS-2004 DM ARP/wARP Automatic solution of protein structures OASIS-2004 DM ARP/wARP by a single run of + + + + Pepstatin-insenstive carboxylproteinase Br-SAD Porcine Pancreatic Elastase Xe-SAD Porcine Pancreatic Elastase Xe-SAD Lysozyme S-SAD Lysozyme S-SAD

13. OASIS-2004 application Contoured at 1  Pepstatin-insenstive carboxylproteinase Space group: P6 2 Unit cell: a = b = 97.31, c = 82.94Å,  = 120 o Resolution limit: 1.8Å; Multiplicity: 5.45 Anomalous scatterer: Br (13) X-rays:  synchrotron radiation  = 0.9191Å;  f ” = 5.0 Bijvoet ratio: / = 7.06% Phasing: OASIS-2004 + DM (Cowtan) Model building: ARP/wARP found 358 of the total 372 residues Data courtesy of Dr. Z. Dauter, National Cancer Institute, USA

14. OASIS-2004 application Contoured at 1  Porcine Pancreatic Elastase Space group: P2 1 2 1 2 1 Unit cell: a = 50.2, b = 58.1, c = 74.3Å Resolution limit: 1.94Å; Total rotation range: 360 o Anomalous scatterer: Xe (1) X-rays:  synchrotron radiation  = 2.1Å;  f ” = 11.8 Bijvoet ratio: / = 5.76% Phasing: OASIS-2004 + DM (Cowtan) Model building: ARP/wARP found 236 of the total 240 residues Data courtesy of Dr. M. S. Weiss, EMBL Hamburg Outstation, c/o DESY, Germany

15. OASIS-2004 application Contoured at 1  Lysozyme Space group: P4 3 2 1 2 Unit cell: a = 78.81, c = 36.80Å Atoms in the asymmetric unit: 1001 Resolution limit: 1.53Å; Multiplicity: 23 Anomalous scatterer: S (10), Cl (7) X-rays:  synchrotron radiation  = 1.54Å;  f ” = 0.56, 0.70 Bijvoet ratio: / = 1.55% Phasing: OASIS-2004 + DM (Cowtan) Model building: ARP/wARP found 128 of the total 129 residues Data courtesy of Dr. Z. Dauter, National Cancer Institute, USA

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

17. Glucose isomerase S-SAD Cu-K  17% Cycle 0 97% Cycle 6 Glucose isomerase S-SAD Cu-K  Cr-K  Se, S-SAD Alanine racemase Cycle 0 52% Cr-K  Se, S-SAD Alanine racemase Cycle 4 97% 25% Cycle 0 Xylanase S-SAD Synchrotron = 1.49Å Xylanase S-SAD Synchrotron = 1.49Å 99% Cycle 6 52% Cycle 0 Lysozyme S-SAD Cr-K  Lysozyme S-SAD Cr-K  98% Cycle 6 Azurin Cu-SAD Synchrotron = 0.97Å Cycle 0 42% Azurin Cu-SAD Synchrotron = 0.97Å Cycle 3 95%

19. OASIS-2004 application Contoured at 1  Xylanase Space group: P2 1 Unit cell: a = 41.07, b = 67.14, c = 50.81Å  = 113.5 o Resolution limit: 1.75Å; Multiplicity: 15.9 Anomalous scatterer: S (5 ) X-rays:  synchrotron radiation  = 1.488Å;  f ” = 0.52 Bijvoet ratio: / = 0.56% Phasing: OASIS-2004 + DM (Cowtan) Model building: RESOLVE BUILD & ARP/wARP found 299 of the total 303 residues at the 6 th cycle of iteration Data courtesy of Dr. Z. Dauter, National Cancer Institute, USA

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

21. Thank you!