OASIS-2006 Institute of Physics Chinese Academy of Sciences Beijing , P.R. China Institute of Physics Chinese Academy of Sciences Beijing , P.R. China

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

OASIS-2006 GUI for CCP4i OASIS-2006 GUI for CCP4i

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

Why direct methods? For better initial SAD phases! For better initial SAD phases!

Bimodal distribution from 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 + -modified phases P+P+ + P P Sim P Bimodal Sim-modified phases P+P+ P Sim P Cochran

Comparison of 4 typical reflections from the protein histone methyltransferase SET 7/9

Comparison of cumulative phase errors in descending order of F obs Comparison of cumulative phase errors in descending order of F obs Errors of P + -modified phases ( o ) Number of reflections Errors of Sim-modified phases ( o ) Histone methyltransferase SET 7/9

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

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

OASIS Applications

Ab initio SAD phasing with weak anomalous signal with weak anomalous signal

SHARP-SOLOMON-ARP/wARP Xylanase Space group: P2 1 Unit cell: a = 41.07, b = 67.14, c = 50.81Å  = o Number of residues in the ASU: 303 Resolution limit: 1.75Å; Multiplicity: 15.9 Anomalous scatterer: S (5 ) X-rays:  synchrotron radiation  = 1.488Å;  f ” = 0.52 Bijvoet ratio: / = 0.56% Data courtesy of Dr. Z. Dauter, National Cancer Institute, USA OASIS-DM-RESOLVE BUILD cycle 0 25% OASIS-DM-ARP/wARP cycle 6 99% SHARP-DM-RESOLVE BUILD BP3-DM-RESOLVE BUILD

2.1Å 3.5Å 4.0Å SAD phasing at different resolutions TT0570 Cu-K  data, / ~ 0.55% SAD phasing at different resolutions TT0570 Cu-K  data, / ~ 0.55%

OASIS + DM SOLVE/RESOLVE results improved by

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

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

SOLVE/RESOLVE mapSigma_A mapOASIS-DM map Dual-space fragment extension based on SOLVE/RESOLVE results 2GW1 3.3Å SAD data

Molecular replacement Fragment extension based on

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

Fragment Extension Dual-space without SAD/SIR information

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

P + > 0.5  ”  model P + < 0.5  ”   model    ~   ~   ”” 

Sample: 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 Resolution range: – 2.10Å Number of reflections: 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 Resolution range: – 2.10Å Number of reflections: 16460

Range of phase error in degrees Cycle 1Cycle 3Cycle 5Cycle 7 Nr. of Reflns. % of P + > ½ Nr. of Reflns. % of P + > ½ Nr. of Reflns. % of P + > ½ Nr. of Reflns. % of P + > ½ UJZ Phase Statistics

DM-ARP/wARP-OASIS iteration DM-ARP/wARP-OASIS iteration Cycle 1 Cycle 2 Cycle 3 Cycle 5 Cycle 7 1UJZ Final model Final model 215 residues MR model MR model 54 residues DM-ARP/wARP iteration DM-ARP/wARP iteration Cycle 4

Hai-fu Fan 1, Yuan-xin Gu 1, Tao Jiang 2, Zheng-jiong Lin 2 & Chao-de Zheng 1 Hai-fu Fan 1, Yuan-xin Gu 1, Tao Jiang 2, Zheng-jiong Lin 2 & Chao-de Zheng 1 Participants of this project Staffs Ph.D. students Jian-rong Chen 1, Qiang Chen 3, Yao He 1, Sheng Huang 1,4, He Li 2, Jia-wei Wang 1, Li-jie Wu 1, De-qiang Yao 1,5 & Tao Zhang 1,6 Jian-rong Chen 1, Qiang Chen 3, Yao He 1, Sheng Huang 1,4, He Li 2, Jia-wei Wang 1, Li-jie Wu 1, De-qiang Yao 1,5 & Tao Zhang 1,6 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 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

SAD data used in this presentation were kindly provided by SAD data used in this presentation were kindly provided by Acknowledgements Dr. Z. Dauter 1, Dr. S. J. Gamblin 2, Dr. B. D. Sha 3, Prof. I. Tanaka 4, Dr. N. Watanabe 4 & Dr. B. Xiao 2 Dr. Z. Dauter 1, Dr. S. J. Gamblin 2, Dr. B. D. Sha 3, Prof. I. Tanaka 4, Dr. N. Watanabe 4 & Dr. B. Xiao 2 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 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

Thank you!