OASIS-2006OASIS-2006Institute of Physics

Chinese Academy of SciencesBeijing 100080, P.R. China

Institute of PhysicsChinese Academy of Sciences

Beijing 100080, P.R. China

http://cryst.iphy.ac.cnhttp://cryst.iphy.ac.cn

OASIS (2000)OASIS (2000) in CCP4in CCP4

OASIS-2004OASIS-2004 on the Webon the Web

OASIS-2006OASIS-2006 on the Websoon

on the Websoon

OASIS-2006 GUI for CCP4iOASIS-2006 GUI for CCP4i

1. Direct-method

2. Reciprocal-space

1. Direct-method

2. Reciprocal-space

Functions of OASIS Functions of OASIS

SAD/SIR PhasingSAD/SIR Phasing

Fragment ExtensionFragment ExtensionFragment ExtensionFragment ExtensionDual-spaceDual-space

by combining with

DM, RESOLVE and ARP/wARPby combining with

DM, RESOLVE and ARP/wARP

Why direct methods?Why direct methods?

For better initial SAD phases!

For better initial SAD phases!

Bimodal distributionfrom SAD

" " "

The phase ofF”

P

Phase information available in SAD

Cochrandistribution

Peaked atany where

from 0 to 2

Peaked at

"2

Sim distribution

Two different kinds of initial SAD phases

P+-modified phases

P++P

PSim PBimodal Sim-modified phases

P+

PSim PCochran

" h h h1

" is the phase of " "exp 2N

j jj

i f i

h h h rF

1 1cos 2 " cos2 "

F h

h h h hh

F F FF

2 ' 'E E E h h h h 3 ' '" " " h h h h

1tan( ) 2 ( ) sin cos

2best P

h h h h

1

2 21 1exp 2 2 1 cos2 cos2

2 2m P

2h h h h h

,

2 2

2U T

pN N

j jj j

E E

Z Z

h h ' " h h h

, 3

1 1tanh sin

2 2

sin sin

c

best best

P

m m

h h

h' h h' h h' h' h h' hh'

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

Comparison of cumulative phase errors in descending order of Fobs

Comparison of cumulative phase errors in descending order of Fobs

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 PErrors of P++-modified -modified

phases phases (( oo ))Number of reflectionsNumber of reflections Errors of Sim-modified Errors of Sim-modified

phases phases (( oo ))

Histone methyltransferase SET 7/9

Why dual-space?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 extensionDual-space fragment extension

, 3

1 1tanh sin

2 2

s s inin

best best

P

m m

h h

h' h h' h h' h' hh h'h'

, 3

1 1tanh sin

2 2

s s inin

best best

P

m m

h h

h' h h' h h' h' hh h'h'

Real-spacefragment extension

RESOLVE BUILD and/or ARP/wARP

Real-spacefragment extension

RESOLVE BUILD and/or ARP/wARP

Partialstructure

Partialstructure

NoNo

YesYes

OK?OK?

EndEnd

PartialmodelPartialmodel

OASIS ApplicationsOASIS Applications

Ab initio SAD phasingAb initio SAD phasingwith

weak anomalous signalwith

weak anomalous signal

SHARP-SOLOMON-ARP/wARPSHARP-SOLOMON-ARP/wARP

XylanaseSpace group: P21 Unit cell: a = 41.07, b = 67.14, c = 50.81Å = 113.5o Number of residues in the ASU: 303 Resolution limit: 1.75Å; Multiplicity: 15.9Anomalous scatterer: S (5 ) X-rays:synchrotron radiation= 1.488Å; f ” = 0.52Bijvoet ratio: <|F |>/<F > = 0.56% Data courtesy of Dr. Z. Dauter, National Cancer Institute, USA

OASIS-DM-RESOLVE BUILDcycle 025%

OASIS-DM-ARP/wARPcycle 699%SHARP-DM-RESOLVE BUILDBP3-DM-RESOLVE BUILD

2.1Å 3.5Å 4.0Å

SAD phasing at different resolutionsTT0570 Cu-Kdata, <|F|>/<F> ~ 0.55%

SAD phasing at different resolutionsTT0570 Cu-Kdata, <|F|>/<F> ~ 0.55%

OASIS + DM OASIS + DM

SOLVE/RESOLVE resultsSOLVE/RESOLVE results

improved byimproved by

SOLVE/RESOLVE

SOLVE/RESOLVE +OASIS-DM-(RESOLVE BUILD)

Dual-space fragment extension based on SOLVE/RESOLVE resultsDual-space fragment extension based on SOLVE/RESOLVE results1LIA (d14) 2.8Å SIR data

SOLVE/RESOLVE map

Sigma_A map based on a model manually builtfrom the SOLVE/RESOLVE map

OASIS-DM mapbased on

the same model

Dual-space fragment extension based on SOLVE/RESOLVE resultsDual-space fragment extension based on SOLVE/RESOLVE results2GW1 3.3Å SAD data

SOLVE/RESOLVE map Sigma_A map OASIS-DM map

Dual-space fragment extension based on SOLVE/RESOLVE resultsDual-space fragment extension based on SOLVE/RESOLVE results2GW1 3.3Å SAD data

Molecular replacement Molecular replacement

Fragment extensionFragment extension

based onbased on

Fragment extension based on

molecular replacement

Finalmodel

acidic phospholipase A2124 residues

MRmodel

60 residues48 residues

DM-ARP/wARP-OASIS iteration

Cycle 1 Cycle 2 Cycle 3

DM-ARP/wARP iteration

Cycle 9 Cycle 11 Cycle 13

DM-ARP/wARP iteration

Fragment ExtensionFragment ExtensionDual-spaceDual-space

without SAD/SIR informationwithout SAD/SIR information

, 3

1 1tanh sin

2 2

sin si n

best best

P

m m

h h

h' h h' h h' h' hh h'h'

, 3

1 1tanh sin

2 2

sin si n

best best

P

m m

h h

h' h h' h h' h' hh h'h'

Partialstructure

Partialstructure " h 5%

the phase of atoms

randomly selected from the current model

" h 5%

the phase of atoms

randomly selected from the current model

" h h h" h h h

" . . "model modeli e h h h h" . . "model modeli e h h h h

Density modification

by DM

Density modification

by DM

NoNo

MRmodel

MRmodel

Phase improvement

by OASIS

Phase improvement

by OASISYesYes

EndEnd

Model building by

RESOLVE BUILD or ARP/wARP

Model building by

RESOLVE BUILD or ARP/wARP

OK?OK?

P+ > 0.5

” model

P+ < 0.5

” model

<||> ~

<||> ~

”

Sample: 1UJZSample: 1UJZSpace group: I 222Unit cell: a=62.88, b=74.55, c=120.44ÅNumber of residues in ASU: 215 molecule A: 87 residues molecule B: 128 residuesResolution range: 37.57 – 2.10ÅNumber of reflections: 16460

Space group: I 222Unit cell: a=62.88, b=74.55, c=120.44ÅNumber of residues in ASU: 215 molecule A: 87 residues molecule B: 128 residuesResolution range: 37.57 – 2.10ÅNumber of reflections: 16460

Range of phase error in degrees

Cycle 1 Cycle 3 Cycle 5 Cycle 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

0 - 30 4084 63 4571 69 4877 71 7226 82

30 - 60 3117 55 3262 57 3204 55 2490 47

60 - 90 2476 44 2330 41 2141 38 1622 21

90 - 120 2025 34 1873 30 1846 27 1466 12

120 -150 1881 31 1711 25 1667 22 1332 7

150 - 180 1766 25 1610 23 1610 17 1215 7

1UJZ Phase Statistics1UJZ Phase Statistics

DM-ARP/wARP-OASISiterationDM-ARP/wARP-OASISiteration

Cycle 1 Cycle 2 Cycle 3 Cycle 5 Cycle 7

1UJZ

FinalmodelFinalmodel215 residues

MRmodelMRmodel

54 residuesDM-ARP/wARP

iterationDM-ARP/wARP

iteration

Cycle 4

Hai-fu Fan1, Yuan-xin Gu1, Tao Jiang2, Zheng-jiong Lin2 & Chao-de Zheng1

Hai-fu Fan1, Yuan-xin Gu1, Tao Jiang2, Zheng-jiong Lin2 & Chao-de Zheng1

Participants of this projectParticipants of this projectStaffsStaffs

Ph.D. studentsPh.D. studentsJian-rong Chen1, Qiang Chen3, Yao He1,

Sheng Huang1,4, He Li2, Jia-wei Wang1, Li-jie Wu1, De-qiang Yao1,5 & Tao Zhang1,6

Jian-rong Chen1, Qiang Chen3, Yao He1, Sheng Huang1,4, He Li2, Jia-wei Wang1, Li-jie Wu1,

De-qiang Yao1,5 & Tao Zhang1,6

1 Institute of Physics, CAS, Beijing, China2 Institute of Biophysics, CAS, Beijing, China3 Peking University, Beijing, China4 Institute of High Energy Physics, CAS, Beijing, China5 Univ. of Science & Technology of China, Hefei, China6 Lanzhou University, Lanzhou, China

1 Institute of Physics, CAS, Beijing, China2 Institute of Biophysics, CAS, Beijing, China3 Peking University, Beijing, China4 Institute of High Energy Physics, CAS, Beijing, China5 Univ. of Science & Technology of China, Hefei, China6 Lanzhou University, Lanzhou, China

SAD data used in this presentationwere kindly provided by

SAD data used in this presentationwere kindly provided by

AcknowledgementsAcknowledgements

Dr. Z. Dauter1, Dr. S. J. Gamblin2, Dr. B. D. Sha3, Prof. I. Tanaka4, Dr. N. Watanabe4 & Dr. B. Xiao2

Dr. Z. Dauter1, Dr. S. J. Gamblin2, Dr. B. D. Sha3, Prof. I. Tanaka4, Dr. N. Watanabe4 & Dr. B. Xiao2

1 Argonne National Laboratory, USA2 The National Institute for Medical Research, UK3 Department of Cell Biology, University of Alabama at Birmingham, USA4 Graduate School of Science, Hokkaido University, Japan

1 Argonne National Laboratory, USA2 The National Institute for Medical Research, UK3 Department of Cell Biology, University of Alabama at Birmingham, USA4 Graduate School of Science, Hokkaido University, Japan

Thank you!Thank you!