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

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

OASIS-2004 application Contoured at 1  Xylanase Space group: P2 1 Unit cell: a = 41.07, b = 67.14, c = 50.81Å  = 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 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

TT0570 Data courtesy of Professor Isao Tanaka & Dr. Nobuhisa Watanabe Graduate School of Science, Hokkaido University, Japan Space group: P Unit cell: a = b = c = Å Number of residues in the ASU: 1206 Resolution range: Å Multiplicity: 20.9 Anomalous scatterer: S (22) Wavelength: = 2.291Å;  f ” = 1.14 Bijvoet ratio: / = 1.16% Phasing: OASIS 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

1. Better initial SAD phases

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

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

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

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

Comparison on cumulative phase errors sorted in descending order of F obs Comparison on cumulative phase errors sorted in descending order of F obs Errors of P + -modified phases ( o ) Number of reflections Errors of Sim-modified phases ( o )

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

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

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  = Å;  f ” = 5.0 Bijvoet ratio: / = 7.06% Phasing: OASIS DM (Cowtan) Model building: ARP/wARP found 358 of the total 372 residues Data courtesy of Dr. Z. Dauter, National Cancer Institute, USA

OASIS-2004 application Contoured at 1  Porcine Pancreatic Elastase Space group: P 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 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

OASIS-2004 application Contoured at 1  Lysozyme Space group: P 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 DM (Cowtan) Model building: ARP/wARP found 128 of the total 129 residues Data courtesy of Dr. Z. Dauter, National Cancer Institute, USA

3. Dual-space fragment extension Partial model Partial model Partial model Partial model No Yes Reciprocal-space fragment extension by OASIS DM Reciprocal-space fragment extension by OASIS 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

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%

OASIS-2004 application Contoured at 1  Xylanase Space group: P2 1 Unit cell: a = 41.07, b = 67.14, c = 50.81Å  = 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 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

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

Thank you!